2 See the "run control" section for a working example of the
3 syntax to use when making .mdp entries, with and without detailed
4 documentation for values those entries might take. Everything can
5 be cross-referenced, see the examples there. TODO Make more
8 Molecular dynamics parameters (.mdp options)
9 ============================================
16 Default values are given in parentheses, or listed first among
17 choices. The first option in the list is always the default
18 option. Units are given in square brackets. The difference between a
19 dash and an underscore is ignored.
21 A :ref:`sample mdp file <mdp>` is available. This should be
22 appropriate to start a normal simulation. Edit it to suit your
23 specific needs and desires.
31 directories to include in your topology. Format:
32 ``-I/home/john/mylib -I../otherlib``
36 defines to pass to the preprocessor, default is no defines. You can
37 use any defines to control options in your customized topology
38 files. Options that act on existing :ref:`top` file mechanisms
41 ``-DFLEXIBLE`` will use flexible water instead of rigid water
42 into your topology, this can be useful for normal mode analysis.
44 ``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
45 your topology, used for implementing position restraints.
53 (Despite the name, this list includes algorithms that are not
54 actually integrators over time. :mdp-value:`integrator=steep` and
55 all entries following it are in this category)
59 A leap-frog algorithm for integrating Newton's equations of motion.
63 A velocity Verlet algorithm for integrating Newton's equations
64 of motion. For constant NVE simulations started from
65 corresponding points in the same trajectory, the trajectories
66 are analytically, but not binary, identical to the
67 :mdp-value:`integrator=md` leap-frog integrator. The the kinetic
68 energy, which is determined from the whole step velocities and
69 is therefore slightly too high. The advantage of this integrator
70 is more accurate, reversible Nose-Hoover and Parrinello-Rahman
71 coupling integration based on Trotter expansion, as well as
72 (slightly too small) full step velocity output. This all comes
73 at the cost off extra computation, especially with constraints
74 and extra communication in parallel. Note that for nearly all
75 production simulations the :mdp-value:`integrator=md` integrator
78 .. mdp-value:: md-vv-avek
80 A velocity Verlet algorithm identical to
81 :mdp-value:`integrator=md-vv`, except that the kinetic energy is
82 determined as the average of the two half step kinetic energies
83 as in the :mdp-value:`integrator=md` integrator, and this thus
84 more accurate. With Nose-Hoover and/or Parrinello-Rahman
85 coupling this comes with a slight increase in computational
90 An accurate and efficient leap-frog stochastic dynamics
91 integrator. With constraints, coordinates needs to be
92 constrained twice per integration step. Depending on the
93 computational cost of the force calculation, this can take a
94 significant part of the simulation time. The temperature for one
95 or more groups of atoms (:mdp:`tc-grps`) is set with
96 :mdp:`ref-t`, the inverse friction constant for each group is
97 set with :mdp:`tau-t`. The parameter :mdp:`tcoupl` is
98 ignored. The random generator is initialized with
99 :mdp:`ld-seed`. When used as a thermostat, an appropriate value
100 for :mdp:`tau-t` is 2 ps, since this results in a friction that
101 is lower than the internal friction of water, while it is high
102 enough to remove excess heat NOTE: temperature deviations decay
103 twice as fast as with a Berendsen thermostat with the same
108 An Euler integrator for Brownian or position Langevin dynamics,
109 the velocity is the force divided by a friction coefficient
110 (:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
111 :mdp:`bd-fric` is 0, the friction coefficient for each particle
112 is calculated as mass/ :mdp:`tau-t`, as for the integrator
113 :mdp-value:`integrator=sd`. The random generator is initialized
118 A steepest descent algorithm for energy minimization. The
119 maximum step size is :mdp:`emstep`, the tolerance is
124 A conjugate gradient algorithm for energy minimization, the
125 tolerance is :mdp:`emtol`. CG is more efficient when a steepest
126 descent step is done every once in a while, this is determined
127 by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
128 analysis, which requires a very high accuracy, |Gromacs| should be
129 compiled in double precision.
131 .. mdp-value:: l-bfgs
133 A quasi-Newtonian algorithm for energy minimization according to
134 the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
135 practice this seems to converge faster than Conjugate Gradients,
136 but due to the correction steps necessary it is not (yet)
141 Normal mode analysis is performed on the structure in the :ref:`tpr`
142 file. |Gromacs| should be compiled in double precision.
146 Test particle insertion. The last molecule in the topology is
147 the test particle. A trajectory must be provided to ``mdrun
148 -rerun``. This trajectory should not contain the molecule to be
149 inserted. Insertions are performed :mdp:`nsteps` times in each
150 frame at random locations and with random orientiations of the
151 molecule. When :mdp:`nstlist` is larger than one,
152 :mdp:`nstlist` insertions are performed in a sphere with radius
153 :mdp:`rtpi` around a the same random location using the same
154 neighborlist. Since neighborlist construction is expensive,
155 one can perform several extra insertions with the same list
156 almost for free. The random seed is set with
157 :mdp:`ld-seed`. The temperature for the Boltzmann weighting is
158 set with :mdp:`ref-t`, this should match the temperature of the
159 simulation of the original trajectory. Dispersion correction is
160 implemented correctly for TPI. All relevant quantities are
161 written to the file specified with ``mdrun -tpi``. The
162 distribution of insertion energies is written to the file
163 specified with ``mdrun -tpid``. No trajectory or energy file is
164 written. Parallel TPI gives identical results to single-node
165 TPI. For charged molecules, using PME with a fine grid is most
166 accurate and also efficient, since the potential in the system
167 only needs to be calculated once per frame.
171 Test particle insertion into a predefined cavity location. The
172 procedure is the same as for :mdp-value:`integrator=tpi`, except
173 that one coordinate extra is read from the trajectory, which is
174 used as the insertion location. The molecule to be inserted
175 should be centered at 0,0,0. |Gromacs| does not do this for you,
176 since for different situations a different way of centering
177 might be optimal. Also :mdp:`rtpi` sets the radius for the
178 sphere around this location. Neighbor searching is done only
179 once per frame, :mdp:`nstlist` is not used. Parallel
180 :mdp-value:`integrator=tpic` gives identical results to
181 single-rank :mdp-value:`integrator=tpic`.
186 starting time for your run (only makes sense for time-based
192 time step for integration (only makes sense for time-based
198 maximum number of steps to integrate or minimize, -1 is no
204 The starting step. The time at an step i in a run is
205 calculated as: t = :mdp:`tinit` + :mdp:`dt` *
206 (:mdp:`init-step` + i). The free-energy lambda is calculated
207 as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
208 (:mdp:`init-step` + i). Also non-equilibrium MD parameters can
209 depend on the step number. Thus for exact restarts or redoing
210 part of a run it might be necessary to set :mdp:`init-step` to
211 the step number of the restart frame. :ref:`gmx convert-tpr`
212 does this automatically.
214 .. mdp:: simulation-part
217 A simulation can consist of multiple parts, each of which has
218 a part number. This option specifies what that number will
219 be, which helps keep track of parts that are logically the
220 same simulation. This option is generally useful to set only
221 when coping with a crashed simulation where files were lost.
225 .. mdp-value:: Linear
227 Remove center of mass translational velocity
229 .. mdp-value:: Angular
231 Remove center of mass translational and rotational velocity around
234 .. mdp-value:: Linear-acceleration-correction
236 Remove center of mass translational velocity. Correct the center of
237 mass position assuming linear acceleration over :mdp:`nstcomm` steps.
238 This is useful for cases where an acceleration is expected on the
239 center of mass which is nearly constant over mdp:`nstcomm` steps.
240 This can occur for example when pulling on a group using an absolute
245 No restriction on the center of mass motion
250 frequency for center of mass motion removal
254 group(s) for center of mass motion removal, default is the whole
264 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
265 the friction coefficient for each particle is calculated as mass/
271 used to initialize random generator for thermal noise for
272 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
273 a pseudo random seed is used. When running BD or SD on multiple
274 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
275 the processor number.
283 (10.0) \[kJ mol-1 nm-1\]
284 the minimization is converged when the maximum force is smaller
295 frequency of performing 1 steepest descent step while doing
296 conjugate gradient energy minimization.
301 Number of correction steps to use for L-BFGS minimization. A higher
302 number is (at least theoretically) more accurate, but slower.
305 Shell Molecular Dynamics
306 ^^^^^^^^^^^^^^^^^^^^^^^^
308 When shells or flexible constraints are present in the system the
309 positions of the shells and the lengths of the flexible constraints
310 are optimized at every time step until either the RMS force on the
311 shells and constraints is less than :mdp:`emtol`, or a maximum number
312 of iterations :mdp:`niter` has been reached. Minimization is converged
313 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
314 value should be 1.0 at most.
319 maximum number of iterations for optimizing the shell positions and
320 the flexible constraints.
325 the step size for optimizing the flexible constraints. Should be
326 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
327 particles in a flexible constraint and d2V/dq2 is the second
328 derivative of the potential in the constraint direction. Hopefully
329 this number does not differ too much between the flexible
330 constraints, as the number of iterations and thus the runtime is
331 very sensitive to fcstep. Try several values!
334 Test particle insertion
335 ^^^^^^^^^^^^^^^^^^^^^^^
340 the test particle insertion radius, see integrators
341 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
350 number of steps that elapse between writing coordinates to output
351 trajectory file, the last coordinates are always written
356 number of steps that elapse between writing velocities to output
357 trajectory, the last velocities are always written
362 number of steps that elapse between writing forces to output
368 number of steps that elapse between writing energies to the log
369 file, the last energies are always written
371 .. mdp:: nstcalcenergy
374 number of steps that elapse between calculating the energies, 0 is
375 never. This option is only relevant with dynamics. This option affects the
376 performance in parallel simulations, because calculating energies
377 requires global communication between all processes which can
378 become a bottleneck at high parallelization.
383 number of steps that else between writing energies to energy file,
384 the last energies are always written, should be a multiple of
385 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
386 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
387 energy file, so :ref:`gmx energy` can report exact energy averages
388 and fluctuations also when :mdp:`nstenergy` > 1
390 .. mdp:: nstxout-compressed
393 number of steps that elapse between writing position coordinates
394 using lossy compression
396 .. mdp:: compressed-x-precision
399 precision with which to write to the compressed trajectory file
401 .. mdp:: compressed-x-grps
403 group(s) to write to the compressed trajectory file, by default the
404 whole system is written (if :mdp:`nstxout-compressed` > 0)
408 group(s) for which to write to write short-ranged non-bonded
409 potential energies to the energy file (not supported on GPUs)
415 .. mdp:: cutoff-scheme
417 .. mdp-value:: Verlet
419 Generate a pair list with buffering. The buffer size is
420 automatically set based on :mdp:`verlet-buffer-tolerance`,
421 unless this is set to -1, in which case :mdp:`rlist` will be
422 used. This option has an explicit, exact cut-off at :mdp:`rvdw`
423 equal to :mdp:`rcoulomb`, unless PME or Ewald is used, in which
424 case :mdp:`rcoulomb` > :mdp:`rvdw` is allowed. Currently only
425 cut-off, reaction-field, PME or Ewald electrostatics and plain
426 LJ are supported. Some :ref:`gmx mdrun` functionality is not yet
427 supported with the :mdp-value:`cutoff-scheme=Verlet` scheme, but :ref:`gmx grompp`
428 checks for this. Native GPU acceleration is only supported with
429 :mdp-value:`cutoff-scheme=Verlet`. With GPU-accelerated PME or with separate PME
430 ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
431 balance by scaling :mdp:`rcoulomb` and the grid spacing. This
432 can be turned off with ``mdrun -notunepme``. :mdp-value:`cutoff-scheme=Verlet` is
433 faster than :mdp-value:`cutoff-scheme=group` when there is no water, or if
434 :mdp-value:`cutoff-scheme=group` would use a pair-list buffer to conserve energy.
438 Generate a pair list for groups of atoms. These groups
439 correspond to the charge groups in the topology. This was the
440 only cut-off treatment scheme before version 4.6, and is
441 **deprecated in |gmx-version|**. There is no explicit buffering of
442 the pair list. This enables efficient force calculations for
443 water, but energy is only conserved when a buffer is explicitly
452 Frequency to update the neighbor list. When this is 0, the
453 neighbor list is made only once. With energy minimization the
454 neighborlist will be updated for every energy evaluation when
455 :mdp:`nstlist` is greater than 0. With :mdp-value:`cutoff-scheme=Verlet` and
456 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
457 a minimum value and :ref:`gmx mdrun` might increase it, unless
458 it is set to 1. With parallel simulations and/or non-bonded
459 force calculation on the GPU, a value of 20 or 40 often gives
460 the best performance. With :mdp-value:`cutoff-scheme=group` and non-exact
461 cut-off's, :mdp:`nstlist` will affect the accuracy of your
462 simulation and it can not be chosen freely.
466 The neighbor list is only constructed once and never
467 updated. This is mainly useful for vacuum simulations in which
468 all particles see each other.
478 Make a grid in the box and only check atoms in neighboring grid
479 cells when constructing a new neighbor list every
480 :mdp:`nstlist` steps. In large systems grid search is much
481 faster than simple search.
483 .. mdp-value:: simple
485 Check every atom in the box when constructing a new neighbor
486 list every :mdp:`nstlist` steps (only with :mdp-value:`cutoff-scheme=group`
493 Use periodic boundary conditions in all directions.
497 Use no periodic boundary conditions, ignore the box. To simulate
498 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
499 best performance without cut-offs on a single MPI rank, set
500 :mdp:`nstlist` to zero and :mdp:`ns-type` =simple.
504 Use periodic boundary conditions in x and y directions
505 only. This works only with :mdp:`ns-type` =grid and can be used
506 in combination with walls_. Without walls or with only one wall
507 the system size is infinite in the z direction. Therefore
508 pressure coupling or Ewald summation methods can not be
509 used. These disadvantages do not apply when two walls are used.
511 .. mdp:: periodic-molecules
515 molecules are finite, fast molecular PBC can be used
519 for systems with molecules that couple to themselves through the
520 periodic boundary conditions, this requires a slower PBC
521 algorithm and molecules are not made whole in the output
523 .. mdp:: verlet-buffer-tolerance
525 (0.005) \[kJ/mol/ps\]
527 Useful only with the :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`. This sets
528 the maximum allowed error for pair interactions per particle caused
529 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
530 :mdp:`nstlist` and the Verlet buffer size are fixed (for
531 performance reasons), particle pairs not in the pair list can
532 occasionally get within the cut-off distance during
533 :mdp:`nstlist` -1 steps. This causes very small jumps in the
534 energy. In a constant-temperature ensemble, these very small energy
535 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
536 estimate assumes a homogeneous particle distribution, hence the
537 errors might be slightly underestimated for multi-phase
538 systems. (See the `reference manual`_ for details). For longer
539 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
540 overestimated, because the interactions between particles are
541 ignored. Combined with cancellation of errors, the actual drift of
542 the total energy is usually one to two orders of magnitude
543 smaller. Note that the generated buffer size takes into account
544 that the |Gromacs| pair-list setup leads to a reduction in the
545 drift by a factor 10, compared to a simple particle-pair based
546 list. Without dynamics (energy minimization etc.), the buffer is 5%
547 of the cut-off. For NVE simulations the initial temperature is
548 used, unless this is zero, in which case a buffer of 10% is
549 used. For NVE simulations the tolerance usually needs to be lowered
550 to achieve proper energy conservation on the nanosecond time
551 scale. To override the automated buffer setting, use
552 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
557 Cut-off distance for the short-range neighbor list. With the
558 :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`, this is by default set by the
559 :mdp:`verlet-buffer-tolerance` option and the value of
560 :mdp:`rlist` is ignored.
568 .. mdp-value:: Cut-off
570 Plain cut-off with neighborlist radius :mdp:`rlist` and
571 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
576 Classical Ewald sum electrostatics. The real-space cut-off
577 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
578 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
579 of wave vectors used in reciprocal space is controlled by
580 :mdp:`fourierspacing`. The relative accuracy of
581 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
583 NOTE: Ewald scales as O(N^3/2) and is thus extremely slow for
584 large systems. It is included mainly for reference - in most
585 cases PME will perform much better.
589 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
590 space is similar to the Ewald sum, while the reciprocal part is
591 performed with FFTs. Grid dimensions are controlled with
592 :mdp:`fourierspacing` and the interpolation order with
593 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
594 interpolation the electrostatic forces have an accuracy of
595 2-3*10^-4. Since the error from the vdw-cutoff is larger than
596 this you might try 0.15 nm. When running in parallel the
597 interpolation parallelizes better than the FFT, so try
598 decreasing grid dimensions while increasing interpolation.
600 .. mdp-value:: P3M-AD
602 Particle-Particle Particle-Mesh algorithm with analytical
603 derivative for for long range electrostatic interactions. The
604 method and code is identical to SPME, except that the influence
605 function is optimized for the grid. This gives a slight increase
608 .. mdp-value:: Reaction-Field
610 Reaction field electrostatics with Coulomb cut-off
611 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
612 dielectric constant beyond the cut-off is
613 :mdp:`epsilon-rf`. The dielectric constant can be set to
614 infinity by setting :mdp:`epsilon-rf` =0.
616 .. mdp-value:: Generalized-Reaction-Field
618 Generalized reaction field with Coulomb cut-off
619 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rcoulomb`. The
620 dielectric constant beyond the cut-off is
621 :mdp:`epsilon-rf`. The ionic strength is computed from the
622 number of charged (*i.e.* with non zero charge) charge
623 groups. The temperature for the GRF potential is set with
626 .. mdp-value:: Reaction-Field-zero
628 In |Gromacs|, normal reaction-field electrostatics with
629 :mdp:`cutoff-scheme` = :mdp-value:`cutoff-scheme=group` leads to bad energy
630 conservation. :mdp-value:`coulombtype=Reaction-Field-zero` solves this by making
631 the potential zero beyond the cut-off. It can only be used with
632 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
633 only for that value the force vanishes at the
634 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
635 :mdp:`rcoulomb` to accommodate for the size of charge groups
636 and diffusion between neighbor list updates. This, and the fact
637 that table lookups are used instead of analytical functions make
638 :mdp-value:`coulombtype=Reaction-Field-zero` computationally more expensive than
639 normal reaction-field.
643 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
644 might want to use :mdp-value:`coulombtype=Reaction-Field-zero` instead, which has
645 a similar potential shape, but has a physical interpretation and
646 has better energies due to the exclusion correction terms.
648 .. mdp-value:: Encad-Shift
650 The Coulomb potential is decreased over the whole range, using
651 the definition from the Encad simulation package.
653 .. mdp-value:: Switch
655 Analogous to :mdp-value:`vdwtype=Switch` for
656 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
657 serious artifacts, advice: use :mdp-value:`coulombtype=Reaction-Field-zero`
662 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
663 with user-defined potential functions for repulsion, dispersion
664 and Coulomb. When pair interactions are present, :ref:`gmx
665 mdrun` also expects to find a file ``tablep.xvg`` for the pair
666 interactions. When the same interactions should be used for
667 non-bonded and pair interactions the user can specify the same
668 file name for both table files. These files should contain 7
669 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
670 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
671 function, ``g(x)`` the dispersion function and ``h(x)`` the
672 repulsion function. When :mdp:`vdwtype` is not set to User the
673 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
674 the non-bonded interactions ``x`` values should run from 0 to
675 the largest cut-off distance + :mdp:`table-extension` and
676 should be uniformly spaced. For the pair interactions the table
677 length in the file will be used. The optimal spacing, which is
678 used for non-user tables, is ``0.002 nm`` when you run in mixed
679 precision or ``0.0005 nm`` when you run in double precision. The
680 function value at ``x=0`` is not important. More information is
681 in the printed manual.
683 .. mdp-value:: PME-Switch
685 A combination of PME and a switch function for the direct-space
686 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
687 :mdp:`rlist`. This is mainly useful constant energy simulations
688 (note that using PME with :mdp:`cutoff-scheme` = :mdp-value:`cutoff-scheme=Verlet`
689 will be more efficient).
691 .. mdp-value:: PME-User
693 A combination of PME and user tables (see
694 above). :mdp:`rcoulomb` is allowed to be smaller than
695 :mdp:`rlist`. The PME mesh contribution is subtracted from the
696 user table by :ref:`gmx mdrun`. Because of this subtraction the
697 user tables should contain about 10 decimal places.
699 .. mdp-value:: PME-User-Switch
701 A combination of PME-User and a switching function (see
702 above). The switching function is applied to final
703 particle-particle interaction, *i.e.* both to the user supplied
704 function and the PME Mesh correction part.
706 .. mdp:: coulomb-modifier
708 .. mdp-value:: Potential-shift-Verlet
710 Selects Potential-shift with the Verlet cutoff-scheme, as it is
711 (nearly) free; selects None with the group cutoff-scheme.
713 .. mdp-value:: Potential-shift
715 Shift the Coulomb potential by a constant such that it is zero
716 at the cut-off. This makes the potential the integral of the
717 force. Note that this does not affect the forces or the
722 Use an unmodified Coulomb potential. With the group scheme this
723 means no exact cut-off is used, energies and forces are
724 calculated for all pairs in the neighborlist.
726 .. mdp:: rcoulomb-switch
729 where to start switching the Coulomb potential, only relevant
730 when force or potential switching is used
735 distance for the Coulomb cut-off
740 The relative dielectric constant. A value of 0 means infinity.
745 The relative dielectric constant of the reaction field. This
746 is only used with reaction-field electrostatics. A value of 0
755 .. mdp-value:: Cut-off
757 Twin range cut-offs with neighbor list cut-off :mdp:`rlist` and
758 VdW cut-off :mdp:`rvdw`, where :mdp:`rvdw` >= :mdp:`rlist`.
762 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
763 grid dimensions are controlled with :mdp:`fourierspacing` in
764 the same way as for electrostatics, and the interpolation order
765 is controlled with :mdp:`pme-order`. The relative accuracy of
766 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
767 and the specific combination rules that are to be used by the
768 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
772 This functionality is deprecated and replaced by
773 :mdp:`vdw-modifier` = Force-switch. The LJ (not Buckingham)
774 potential is decreased over the whole range and the forces decay
775 smoothly to zero between :mdp:`rvdw-switch` and
776 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
777 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
778 size of charge groups and diffusion between neighbor list
781 .. mdp-value:: Switch
783 This functionality is deprecated and replaced by
784 :mdp:`vdw-modifier` = Potential-switch. The LJ (not Buckingham)
785 potential is normal out to :mdp:`rvdw-switch`, after which it
786 is switched off to reach zero at :mdp:`rvdw`. Both the
787 potential and force functions are continuously smooth, but be
788 aware that all switch functions will give rise to a bulge
789 (increase) in the force (since we are switching the
790 potential). The neighbor search cut-off :mdp:`rlist` should be
791 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
792 size of charge groups and diffusion between neighbor list
795 .. mdp-value:: Encad-Shift
797 The LJ (not Buckingham) potential is decreased over the whole
798 range, using the definition from the Encad simulation package.
802 See user for :mdp:`coulombtype`. The function value at zero is
803 not important. When you want to use LJ correction, make sure
804 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
805 function. When :mdp:`coulombtype` is not set to User the values
806 for the ``f`` and ``-f'`` columns are ignored.
808 .. mdp:: vdw-modifier
810 .. mdp-value:: Potential-shift-Verlet
812 Selects Potential-shift with the Verlet cutoff-scheme, as it is
813 (nearly) free; selects None with the group cutoff-scheme.
815 .. mdp-value:: Potential-shift
817 Shift the Van der Waals potential by a constant such that it is
818 zero at the cut-off. This makes the potential the integral of
819 the force. Note that this does not affect the forces or the
824 Use an unmodified Van der Waals potential. With the group scheme
825 this means no exact cut-off is used, energies and forces are
826 calculated for all pairs in the neighborlist.
828 .. mdp-value:: Force-switch
830 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
831 and :mdp:`rvdw`. This shifts the potential shift over the whole
832 range and switches it to zero at the cut-off. Note that this is
833 more expensive to calculate than a plain cut-off and it is not
834 required for energy conservation, since Potential-shift
835 conserves energy just as well.
837 .. mdp-value:: Potential-switch
839 Smoothly switches the potential to zero between
840 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
841 articifically large forces in the switching region and is much
842 more expensive to calculate. This option should only be used if
843 the force field you are using requires this.
849 where to start switching the LJ force and possibly the potential,
850 only relevant when force or potential switching is used
855 distance for the LJ or Buckingham cut-off
861 don't apply any correction
863 .. mdp-value:: EnerPres
865 apply long range dispersion corrections for Energy and Pressure
869 apply long range dispersion corrections for Energy only
875 .. mdp:: table-extension
878 Extension of the non-bonded potential lookup tables beyond the
879 largest cut-off distance. The value should be large enough to
880 account for charge group sizes and the diffusion between
881 neighbor-list updates. Without user defined potential the same
882 table length is used for the lookup tables for the 1-4
883 interactions, which are always tabulated irrespective of the use of
884 tables for the non-bonded interactions. The value of
885 :mdp:`table-extension` in no way affects the values of
886 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
888 .. mdp:: energygrp-table
890 When user tables are used for electrostatics and/or VdW, here one
891 can give pairs of energy groups for which seperate user tables
892 should be used. The two energy groups will be appended to the table
893 file name, in order of their definition in :mdp:`energygrps`,
894 seperated by underscores. For example, if ``energygrps = Na Cl
895 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
896 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
897 normal ``table.xvg`` which will be used for all other energy group
904 .. mdp:: fourierspacing
907 For ordinary Ewald, the ratio of the box dimensions and the spacing
908 determines a lower bound for the number of wave vectors to use in
909 each (signed) direction. For PME and P3M, that ratio determines a
910 lower bound for the number of Fourier-space grid points that will
911 be used along that axis. In all cases, the number for each
912 direction can be overridden by entering a non-zero value for that
913 :mdp:`fourier-nx` direction. For optimizing the relative load of
914 the particle-particle interactions and the mesh part of PME, it is
915 useful to know that the accuracy of the electrostatics remains
916 nearly constant when the Coulomb cut-off and the PME grid spacing
917 are scaled by the same factor.
924 Highest magnitude of wave vectors in reciprocal space when using Ewald.
925 Grid size when using PME or P3M. These values override
926 :mdp:`fourierspacing` per direction. The best choice is powers of
927 2, 3, 5 and 7. Avoid large primes.
932 Interpolation order for PME. 4 equals cubic interpolation. You
933 might try 6/8/10 when running in parallel and simultaneously
934 decrease grid dimension.
939 The relative strength of the Ewald-shifted direct potential at
940 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
941 will give a more accurate direct sum, but then you need more wave
942 vectors for the reciprocal sum.
944 .. mdp:: ewald-rtol-lj
947 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
948 to control the relative strength of the dispersion potential at
949 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
950 electrostatic potential.
952 .. mdp:: lj-pme-comb-rule
955 The combination rules used to combine VdW-parameters in the
956 reciprocal part of LJ-PME. Geometric rules are much faster than
957 Lorentz-Berthelot and usually the recommended choice, even when the
958 rest of the force field uses the Lorentz-Berthelot rules.
960 .. mdp-value:: Geometric
962 Apply geometric combination rules
964 .. mdp-value:: Lorentz-Berthelot
966 Apply Lorentz-Berthelot combination rules
968 .. mdp:: ewald-geometry
972 The Ewald sum is performed in all three dimensions.
976 The reciprocal sum is still performed in 3D, but a force and
977 potential correction applied in the `z` dimension to produce a
978 pseudo-2D summation. If your system has a slab geometry in the
979 `x-y` plane you can try to increase the `z`-dimension of the box
980 (a box height of 3 times the slab height is usually ok) and use
983 .. mdp:: epsilon-surface
986 This controls the dipole correction to the Ewald summation in
987 3D. The default value of zero means it is turned off. Turn it on by
988 setting it to the value of the relative permittivity of the
989 imaginary surface around your infinite system. Be careful - you
990 shouldn't use this if you have free mobile charges in your
991 system. This value does not affect the slab 3DC variant of the long
1002 No temperature coupling.
1004 .. mdp-value:: berendsen
1006 Temperature coupling with a Berendsen-thermostat to a bath with
1007 temperature :mdp:`ref-t`, with time constant
1008 :mdp:`tau-t`. Several groups can be coupled separately, these
1009 are specified in the :mdp:`tc-grps` field separated by spaces.
1011 .. mdp-value:: nose-hoover
1013 Temperature coupling using a Nose-Hoover extended ensemble. The
1014 reference temperature and coupling groups are selected as above,
1015 but in this case :mdp:`tau-t` controls the period of the
1016 temperature fluctuations at equilibrium, which is slightly
1017 different from a relaxation time. For NVT simulations the
1018 conserved energy quantity is written to energy and log file.
1020 .. mdp-value:: andersen
1022 Temperature coupling by randomizing a fraction of the particles
1023 at each timestep. Reference temperature and coupling groups are
1024 selected as above. :mdp:`tau-t` is the average time between
1025 randomization of each molecule. Inhibits particle dynamics
1026 somewhat, but little or no ergodicity issues. Currently only
1027 implemented with velocity Verlet, and not implemented with
1030 .. mdp-value:: andersen-massive
1032 Temperature coupling by randomizing all particles at infrequent
1033 timesteps. Reference temperature and coupling groups are
1034 selected as above. :mdp:`tau-t` is the time between
1035 randomization of all molecules. Inhibits particle dynamics
1036 somewhat, but little or no ergodicity issues. Currently only
1037 implemented with velocity Verlet.
1039 .. mdp-value:: v-rescale
1041 Temperature coupling using velocity rescaling with a stochastic
1042 term (JCP 126, 014101). This thermostat is similar to Berendsen
1043 coupling, with the same scaling using :mdp:`tau-t`, but the
1044 stochastic term ensures that a proper canonical ensemble is
1045 generated. The random seed is set with :mdp:`ld-seed`. This
1046 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1047 simulations the conserved energy quantity is written to the
1048 energy and log file.
1053 The frequency for coupling the temperature. The default value of -1
1054 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1055 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1056 Verlet integrators :mdp:`nsttcouple` is set to 1.
1058 .. mdp:: nh-chain-length
1061 The number of chained Nose-Hoover thermostats for velocity Verlet
1062 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1063 only supports 1. Data for the NH chain variables is not printed to
1064 the :ref:`edr` file, but can be using the ``GMX_NOSEHOOVER_CHAINS``
1065 environment variable
1069 groups to couple to separate temperature baths
1074 time constant for coupling (one for each group in
1075 :mdp:`tc-grps`), -1 means no temperature coupling
1080 reference temperature for coupling (one for each group in
1091 No pressure coupling. This means a fixed box size.
1093 .. mdp-value:: Berendsen
1095 Exponential relaxation pressure coupling with time constant
1096 :mdp:`tau-p`. The box is scaled every timestep. It has been
1097 argued that this does not yield a correct thermodynamic
1098 ensemble, but it is the most efficient way to scale a box at the
1101 .. mdp-value:: Parrinello-Rahman
1103 Extended-ensemble pressure coupling where the box vectors are
1104 subject to an equation of motion. The equation of motion for the
1105 atoms is coupled to this. No instantaneous scaling takes
1106 place. As for Nose-Hoover temperature coupling the time constant
1107 :mdp:`tau-p` is the period of pressure fluctuations at
1108 equilibrium. This is probably a better method when you want to
1109 apply pressure scaling during data collection, but beware that
1110 you can get very large oscillations if you are starting from a
1111 different pressure. For simulations where the exact fluctation
1112 of the NPT ensemble are important, or if the pressure coupling
1113 time is very short it may not be appropriate, as the previous
1114 time step pressure is used in some steps of the |Gromacs|
1115 implementation for the current time step pressure.
1119 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1120 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1121 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1122 time constant :mdp:`tau-p` is the period of pressure
1123 fluctuations at equilibrium. This is probably a better method
1124 when you want to apply pressure scaling during data collection,
1125 but beware that you can get very large oscillations if you are
1126 starting from a different pressure. Currently (as of version
1127 5.1), it only supports isotropic scaling, and only works without
1132 Specifies the kind of isotropy of the pressure coupling used. Each
1133 kind takes one or more values for :mdp:`compressibility` and
1134 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1136 .. mdp-value:: isotropic
1138 Isotropic pressure coupling with time constant
1139 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1140 :mdp:`ref-p` is required.
1142 .. mdp-value:: semiisotropic
1144 Pressure coupling which is isotropic in the ``x`` and ``y``
1145 direction, but different in the ``z`` direction. This can be
1146 useful for membrane simulations. Two values each for
1147 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1148 ``x/y`` and ``z`` directions respectively.
1150 .. mdp-value:: anisotropic
1152 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1153 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1154 respectively. When the off-diagonal compressibilities are set to
1155 zero, a rectangular box will stay rectangular. Beware that
1156 anisotropic scaling can lead to extreme deformation of the
1159 .. mdp-value:: surface-tension
1161 Surface tension coupling for surfaces parallel to the
1162 xy-plane. Uses normal pressure coupling for the `z`-direction,
1163 while the surface tension is coupled to the `x/y` dimensions of
1164 the box. The first :mdp:`ref-p` value is the reference surface
1165 tension times the number of surfaces ``bar nm``, the second
1166 value is the reference `z`-pressure ``bar``. The two
1167 :mdp:`compressibility` values are the compressibility in the
1168 `x/y` and `z` direction respectively. The value for the
1169 `z`-compressibility should be reasonably accurate since it
1170 influences the convergence of the surface-tension, it can also
1171 be set to zero to have a box with constant height.
1176 The frequency for coupling the pressure. The default value of -1
1177 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1178 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1179 Verlet integrators :mdp:`nstpcouple` is set to 1.
1184 The time constant for pressure coupling (one value for all
1187 .. mdp:: compressibility
1190 The compressibility (NOTE: this is now really in bar^-1) For water at 1
1191 atm and 300 K the compressibility is 4.5e-5 bar^-1. The number of
1192 required values is implied by :mdp:`pcoupltype`.
1197 The reference pressure for coupling. The number of required values
1198 is implied by :mdp:`pcoupltype`.
1200 .. mdp:: refcoord-scaling
1204 The reference coordinates for position restraints are not
1205 modified. Note that with this option the virial and pressure
1206 will depend on the absolute positions of the reference
1211 The reference coordinates are scaled with the scaling matrix of
1212 the pressure coupling.
1216 Scale the center of mass of the reference coordinates with the
1217 scaling matrix of the pressure coupling. The vectors of each
1218 reference coordinate to the center of mass are not scaled. Only
1219 one COM is used, even when there are multiple molecules with
1220 position restraints. For calculating the COM of the reference
1221 coordinates in the starting configuration, periodic boundary
1222 conditions are not taken into account.
1228 Simulated annealing is controlled separately for each temperature
1229 group in |Gromacs|. The reference temperature is a piecewise linear
1230 function, but you can use an arbitrary number of points for each
1231 group, and choose either a single sequence or a periodic behaviour for
1232 each group. The actual annealing is performed by dynamically changing
1233 the reference temperature used in the thermostat algorithm selected,
1234 so remember that the system will usually not instantaneously reach the
1235 reference temperature!
1239 Type of annealing for each temperature group
1243 No simulated annealing - just couple to reference temperature value.
1245 .. mdp-value:: single
1247 A single sequence of annealing points. If your simulation is
1248 longer than the time of the last point, the temperature will be
1249 coupled to this constant value after the annealing sequence has
1250 reached the last time point.
1252 .. mdp-value:: periodic
1254 The annealing will start over at the first reference point once
1255 the last reference time is reached. This is repeated until the
1258 .. mdp:: annealing-npoints
1260 A list with the number of annealing reference/control points used
1261 for each temperature group. Use 0 for groups that are not
1262 annealed. The number of entries should equal the number of
1265 .. mdp:: annealing-time
1267 List of times at the annealing reference/control points for each
1268 group. If you are using periodic annealing, the times will be used
1269 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1270 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1271 etc. The number of entries should equal the sum of the numbers
1272 given in :mdp:`annealing-npoints`.
1274 .. mdp:: annealing-temp
1276 List of temperatures at the annealing reference/control points for
1277 each group. The number of entries should equal the sum of the
1278 numbers given in :mdp:`annealing-npoints`.
1280 Confused? OK, let's use an example. Assume you have two temperature
1281 groups, set the group selections to ``annealing = single periodic``,
1282 the number of points of each group to ``annealing-npoints = 3 4``, the
1283 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1284 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1285 will be coupled to 298K at 0ps, but the reference temperature will
1286 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1287 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1288 second group is coupled to 298K at 0ps, it increases linearly to 320K
1289 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1290 decreases to 298K, and then it starts over with the same pattern
1291 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1292 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1302 Do not generate velocities. The velocities are set to zero
1303 when there are no velocities in the input structure file.
1307 Generate velocities in :ref:`gmx grompp` according to a
1308 Maxwell distribution at temperature :mdp:`gen-temp`, with
1309 random seed :mdp:`gen-seed`. This is only meaningful with
1310 integrator :mdp-value:`integrator=md`.
1315 temperature for Maxwell distribution
1320 used to initialize random generator for random velocities,
1321 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1328 .. mdp:: constraints
1332 No constraints except for those defined explicitly in the
1333 topology, *i.e.* bonds are represented by a harmonic (or other)
1334 potential or a Morse potential (depending on the setting of
1335 :mdp:`morse`) and angles by a harmonic (or other) potential.
1337 .. mdp-value:: h-bonds
1339 Convert the bonds with H-atoms to constraints.
1341 .. mdp-value:: all-bonds
1343 Convert all bonds to constraints.
1345 .. mdp-value:: h-angles
1347 Convert all bonds and additionally the angles that involve
1348 H-atoms to bond-constraints.
1350 .. mdp-value:: all-angles
1352 Convert all bonds and angles to bond-constraints.
1354 .. mdp:: constraint-algorithm
1356 .. mdp-value:: LINCS
1358 LINear Constraint Solver. With domain decomposition the parallel
1359 version P-LINCS is used. The accuracy in set with
1360 :mdp:`lincs-order`, which sets the number of matrices in the
1361 expansion for the matrix inversion. After the matrix inversion
1362 correction the algorithm does an iterative correction to
1363 compensate for lengthening due to rotation. The number of such
1364 iterations can be controlled with :mdp:`lincs-iter`. The root
1365 mean square relative constraint deviation is printed to the log
1366 file every :mdp:`nstlog` steps. If a bond rotates more than
1367 :mdp:`lincs-warnangle` in one step, a warning will be printed
1368 both to the log file and to ``stderr``. LINCS should not be used
1369 with coupled angle constraints.
1371 .. mdp-value:: SHAKE
1373 SHAKE is slightly slower and less stable than LINCS, but does
1374 work with angle constraints. The relative tolerance is set with
1375 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1376 does not support constraints between atoms on different nodes,
1377 thus it can not be used with domain decompositon when inter
1378 charge-group constraints are present. SHAKE can not be used with
1379 energy minimization.
1381 .. mdp:: continuation
1383 This option was formerly known as unconstrained-start.
1387 apply constraints to the start configuration and reset shells
1391 do not apply constraints to the start configuration and do not
1392 reset shells, useful for exact coninuation and reruns
1397 relative tolerance for SHAKE
1399 .. mdp:: lincs-order
1402 Highest order in the expansion of the constraint coupling
1403 matrix. When constraints form triangles, an additional expansion of
1404 the same order is applied on top of the normal expansion only for
1405 the couplings within such triangles. For "normal" MD simulations an
1406 order of 4 usually suffices, 6 is needed for large time-steps with
1407 virtual sites or BD. For accurate energy minimization an order of 8
1408 or more might be required. With domain decomposition, the cell size
1409 is limited by the distance spanned by :mdp:`lincs-order` +1
1410 constraints. When one wants to scale further than this limit, one
1411 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1412 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1413 )* :mdp:`lincs-order` remains constant.
1418 Number of iterations to correct for rotational lengthening in
1419 LINCS. For normal runs a single step is sufficient, but for NVE
1420 runs where you want to conserve energy accurately or for accurate
1421 energy minimization you might want to increase it to 2.
1423 .. mdp:: lincs-warnangle
1426 maximum angle that a bond can rotate before LINCS will complain
1432 bonds are represented by a harmonic potential
1436 bonds are represented by a Morse potential
1439 Energy group exclusions
1440 ^^^^^^^^^^^^^^^^^^^^^^^
1442 .. mdp:: energygrp-excl
1444 Pairs of energy groups for which all non-bonded interactions are
1445 excluded. An example: if you have two energy groups ``Protein`` and
1446 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1447 would give only the non-bonded interactions between the protein and
1448 the solvent. This is especially useful for speeding up energy
1449 calculations with ``mdrun -rerun`` and for excluding interactions
1450 within frozen groups.
1459 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1460 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1461 ``=xy``. When set to 2 pressure coupling and Ewald summation can be
1462 used (it is usually best to use semiisotropic pressure coupling
1463 with the ``x/y`` compressibility set to 0, as otherwise the surface
1464 area will change). Walls interact wit the rest of the system
1465 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1466 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1467 monitor the interaction of energy groups with each wall. The center
1468 of mass motion removal will be turned off in the ``z``-direction.
1470 .. mdp:: wall-atomtype
1472 the atom type name in the force field for each wall. By (for
1473 example) defining a special wall atom type in the topology with its
1474 own combination rules, this allows for independent tuning of the
1475 interaction of each atomtype with the walls.
1481 LJ integrated over the volume behind the wall: 9-3 potential
1485 LJ integrated over the wall surface: 10-4 potential
1489 direct LJ potential with the ``z`` distance from the wall
1493 user defined potentials indexed with the ``z`` distance from the
1494 wall, the tables are read analogously to the
1495 :mdp:`energygrp-table` option, where the first name is for a
1496 "normal" energy group and the second name is ``wall0`` or
1497 ``wall1``, only the dispersion and repulsion columns are used
1499 .. mdp:: wall-r-linpot
1502 Below this distance from the wall the potential is continued
1503 linearly and thus the force is constant. Setting this option to a
1504 postive value is especially useful for equilibration when some
1505 atoms are beyond a wall. When the value is <=0 (<0 for
1506 :mdp:`wall-type` =table), a fatal error is generated when atoms
1509 .. mdp:: wall-density
1512 the number density of the atoms for each wall for wall types 9-3
1515 .. mdp:: wall-ewald-zfac
1518 The scaling factor for the third box vector for Ewald summation
1519 only, the minimum is 2. Ewald summation can only be used with
1520 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1521 ``=3dc``. The empty layer in the box serves to decrease the
1522 unphysical Coulomb interaction between periodic images.
1528 Note that where pulling coordinate are applicable, there can be more
1529 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1530 variables will exist accordingly. Documentation references to things
1531 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1532 applicable pulling coordinate.
1538 No center of mass pulling. All the following pull options will
1539 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1544 Center of mass pulling will be applied on 1 or more groups using
1545 1 or more pull coordinates.
1547 .. mdp:: pull-cylinder-r
1550 the radius of the cylinder for
1551 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=cylinder`
1553 .. mdp:: pull-constr-tol
1556 the relative constraint tolerance for constraint pulling
1558 .. mdp:: pull-print-com
1562 do not print the COM for any group
1566 print the COM of all groups for all pull coordinates
1568 .. mdp:: pull-print-ref-value
1572 do not print the reference value for each pull coordinate
1576 print the reference value for each pull coordinate
1578 .. mdp:: pull-print-components
1582 only print the distance for each pull coordinate
1586 print the distance and Cartesian components selected in
1587 :mdp:`pull-coord1-dim`
1589 .. mdp:: pull-nstxout
1592 frequency for writing out the COMs of all the pull group (0 is
1595 .. mdp:: pull-nstfout
1598 frequency for writing out the force of all the pulled group
1602 .. mdp:: pull-ngroups
1605 The number of pull groups, not including the absolute reference
1606 group, when used. Pull groups can be reused in multiple pull
1607 coordinates. Below only the pull options for group 1 are given,
1608 further groups simply increase the group index number.
1610 .. mdp:: pull-ncoords
1613 The number of pull coordinates. Below only the pull options for
1614 coordinate 1 are given, further coordinates simply increase the
1615 coordinate index number.
1617 .. mdp:: pull-group1-name
1619 The name of the pull group, is looked up in the index file or in
1620 the default groups to obtain the atoms involved.
1622 .. mdp:: pull-group1-weights
1624 Optional relative weights which are multiplied with the masses of
1625 the atoms to give the total weight for the COM. The number should
1626 be 0, meaning all 1, or the number of atoms in the pull group.
1628 .. mdp:: pull-group1-pbcatom
1631 The reference atom for the treatment of periodic boundary
1632 conditions inside the group (this has no effect on the treatment of
1633 the pbc between groups). This option is only important when the
1634 diameter of the pull group is larger than half the shortest box
1635 vector. For determining the COM, all atoms in the group are put at
1636 their periodic image which is closest to
1637 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1638 atom (number wise) is used. This parameter is not used with
1639 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1640 weighting, which is useful for a group of molecules in a periodic
1641 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1644 .. mdp:: pull-coord1-type
1646 .. mdp-value:: umbrella
1648 Center of mass pulling using an umbrella potential between the
1649 reference group and one or more groups.
1651 .. mdp-value:: constraint
1653 Center of mass pulling using a constraint between the reference
1654 group and one or more groups. The setup is identical to the
1655 option umbrella, except for the fact that a rigid constraint is
1656 applied instead of a harmonic potential.
1658 .. mdp-value:: constant-force
1660 Center of mass pulling using a linear potential and therefore a
1661 constant force. For this option there is no reference position
1662 and therefore the parameters :mdp:`pull-coord1-init` and
1663 :mdp:`pull-coord1-rate` are not used.
1665 .. mdp-value:: flat-bottom
1667 At distances above :mdp:`pull-coord1-init` a harmonic potential
1668 is applied, otherwise no potential is applied.
1670 .. mdp-value:: flat-bottom-high
1672 At distances below :mdp:`pull-coord1-init` a harmonic potential
1673 is applied, otherwise no potential is applied.
1675 .. mdp-value:: external-potential
1677 An external potential that needs to be provided by another
1680 .. mdp:: pull-coord1-potential-provider
1682 The name of the external module that provides the potential for
1683 the case where :mdp:`pull-coord1-type` is external-potential.
1685 .. mdp:: pull-coord1-geometry
1687 .. mdp-value:: distance
1689 Pull along the vector connecting the two groups. Components can
1690 be selected with :mdp:`pull-coord1-dim`.
1692 .. mdp-value:: direction
1694 Pull in the direction of :mdp:`pull-coord1-vec`.
1696 .. mdp-value:: direction-periodic
1698 As :mdp-value:`pull-coord1-geometry=direction`, but allows the distance to be larger
1699 than half the box size. With this geometry the box should not be
1700 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1701 the pull force is not added to virial.
1703 .. mdp-value:: direction-relative
1705 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1706 that points from the COM of a third to the COM of a fourth pull
1707 group. This means that 4 groups need to be supplied in
1708 :mdp:`pull-coord1-groups`. Note that the pull force will give
1709 rise to a torque on the pull vector, which is turn leads to
1710 forces perpendicular to the pull vector on the two groups
1711 defining the vector. If you want a pull group to move between
1712 the two groups defining the vector, simply use the union of
1713 these two groups as the reference group.
1715 .. mdp-value:: cylinder
1717 Designed for pulling with respect to a layer where the reference
1718 COM is given by a local cylindrical part of the reference group.
1719 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1720 the first of the two groups in :mdp:`pull-coord1-groups` a
1721 cylinder is selected around the axis going through the COM of
1722 the second group with direction :mdp:`pull-coord1-vec` with
1723 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1724 continously to zero as the radial distance goes from 0 to
1725 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1726 dependence gives rise to radial forces on both pull groups.
1727 Note that the radius should be smaller than half the box size.
1728 For tilted cylinders they should be even smaller than half the
1729 box size since the distance of an atom in the reference group
1730 from the COM of the pull group has both a radial and an axial
1731 component. This geometry is not supported with constraint
1734 .. mdp-value:: angle
1736 Pull along an angle defined by four groups. The angle is
1737 defined as the angle between two vectors: the vector connecting
1738 the COM of the first group to the COM of the second group and
1739 the vector connecting the COM of the third group to the COM of
1742 .. mdp-value:: angle-axis
1744 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1745 Thus, only the two groups that define the first vector need to be given.
1747 .. mdp-value:: dihedral
1749 Pull along a dihedral angle defined by six groups. These pairwise
1750 define three vectors: the vector connecting the COM of group 1
1751 to the COM of group 2, the COM of group 3 to the COM of group 4,
1752 and the COM of group 5 to the COM group 6. The dihedral angle is
1753 then defined as the angle between two planes: the plane spanned by the
1754 the two first vectors and the plane spanned the two last vectors.
1757 .. mdp:: pull-coord1-groups
1759 The group indices on which this pull coordinate will operate.
1760 The number of group indices required is geometry dependent.
1761 The first index can be 0, in which case an
1762 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1763 absolute reference the system is no longer translation invariant
1764 and one should think about what to do with the center of mass
1767 .. mdp:: pull-coord1-dim
1770 Selects the dimensions that this pull coordinate acts on and that
1771 are printed to the output files when
1772 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1773 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1774 components set to Y contribute to the distance. Thus setting this
1775 to Y Y N results in a distance in the x/y plane. With other
1776 geometries all dimensions with non-zero entries in
1777 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1778 dimensions only affect the output.
1780 .. mdp:: pull-coord1-origin
1783 The pull reference position for use with an absolute reference.
1785 .. mdp:: pull-coord1-vec
1788 The pull direction. :ref:`gmx grompp` normalizes the vector.
1790 .. mdp:: pull-coord1-start
1794 do not modify :mdp:`pull-coord1-init`
1798 add the COM distance of the starting conformation to
1799 :mdp:`pull-coord1-init`
1801 .. mdp:: pull-coord1-init
1803 (0.0) \[nm\] / \[deg\]
1804 The reference distance at t=0.
1806 .. mdp:: pull-coord1-rate
1808 (0) \[nm/ps\] / \[deg/ps\]
1809 The rate of change of the reference position.
1811 .. mdp:: pull-coord1-k
1813 (0) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\]
1814 The force constant. For umbrella pulling this is the harmonic force
1815 constant in kJ mol-1 nm-2 (or kJ mol-1 rad-2 for angles). For constant force pulling this is the
1816 force constant of the linear potential, and thus the negative (!)
1817 of the constant force in kJ mol-1 nm-1 (or kJ mol-1 rad-1 for angles).
1818 Note that for angles the force constant is expressed in terms of radians
1819 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1821 .. mdp:: pull-coord1-kB
1823 (pull-k1) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\]
1824 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1825 :mdp:`free-energy` is turned on. The force constant is then (1 -
1826 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1828 AWH adaptive biasing
1829 ^^^^^^^^^^^^^^^^^^^^
1839 Adaptively bias a reaction coordinate using the AWH method and estimate
1840 the corresponding PMF. The PMF and other AWH data are written to energy
1841 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1842 the ``gmx awh`` tool. The AWH coordinate can be
1843 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1844 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1845 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1848 .. mdp:: awh-potential
1850 .. mdp-value:: convolved
1852 The applied biasing potential is the convolution of the bias function and a
1853 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1854 in a smooth potential function and force. The resolution of the potential is set
1855 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1857 .. mdp-value:: umbrella
1859 The potential bias is applied by controlling the position of an harmonic potential
1860 using Monte-Carlo sampling. The force constant is set with
1861 :mdp:`awh1-dim1-force-constant`. The umbrella location
1862 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1863 There are no advantages to using an umbrella.
1864 This option is mainly for comparison and testing purposes.
1866 .. mdp:: awh-share-multisim
1870 AWH will not share biases across simulations started with
1871 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1875 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1876 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1877 with the biases with the same :mdp:`awh1-share-group` value.
1878 The simulations should have the same AWH settings for sharing to make sense.
1879 :ref:`gmx mdrun` will check whether the simulations are technically
1880 compatible for sharing, but the user should check that bias sharing
1881 physically makes sense.
1885 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1886 where -1 indicates to generate a seed. Only used with
1887 :mdp-value:`awh-potential=umbrella`.
1892 Number of steps between printing AWH data to the energy file, should be
1893 a multiple of :mdp:`nstenergy`.
1895 .. mdp:: awh-nstsample
1898 Number of steps between sampling of the coordinate value. This sampling
1899 is the basis for updating the bias and estimating the PMF and other AWH observables.
1901 .. mdp:: awh-nsamples-update
1904 The number of coordinate samples used for each AWH update.
1905 The update interval in steps is :mdp:`awh-nstsample` times this value.
1910 The number of biases, each acting on its own coordinate.
1911 The following options should be specified
1912 for each bias although below only the options for bias number 1 is shown. Options for
1913 other bias indices are obtained by replacing '1' by the bias index.
1915 .. mdp:: awh1-error-init
1918 Estimated initial average error of the PMF for this bias. This value together with the
1919 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1920 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1922 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1923 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1924 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1925 then :mdp:`awh1-error-init` should reflect that knowledge.
1927 .. mdp:: awh1-growth
1929 .. mdp-value:: exp-linear
1931 Each bias keeps a reference weight histogram for the coordinate samples.
1932 Its size sets the magnitude of the bias function and free energy estimate updates
1933 (few samples corresponds to large updates and vice versa).
1934 Thus, its growth rate sets the maximum convergence rate.
1935 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1936 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1937 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1938 high free energy barriers have not yet been flattened by the bias.
1940 .. mdp-value:: linear
1942 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1943 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
1944 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
1946 .. mdp:: awh1-equilibrate-histogram
1950 Do not equilibrate histogram.
1954 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
1955 histogram of sampled weights is following the target distribution closely enough (specifically,
1956 at least 80% of the target region needs to have a local relative error of less than 20%). This
1957 option would typically only be used when :mdp:`awh1-share-group` > 0
1958 and the initial configurations poorly represent the target
1961 .. mdp:: awh1-target
1963 .. mdp-value:: constant
1965 The bias is tuned towards a constant (uniform) coordinate distribution
1966 in the defined sampling interval (defined by \[:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`\]).
1968 .. mdp-value:: cutoff
1970 Similar to :mdp-value:`awh1-target=constant`, but the target
1971 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
1972 where F is the free energy relative to the estimated global minimum.
1973 This provides a smooth switch of a flat target distribution in
1974 regions with free energy lower than the cut-off to a Boltzmann
1975 distribution in regions with free energy higher than the cut-off.
1977 .. mdp-value:: boltzmann
1979 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
1980 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
1981 would give the same coordinate distribution as sampling with a simulation temperature
1984 .. mdp-value:: local-boltzmann
1986 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
1987 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
1988 change of the bias only depends on the local sampling. This local convergence property is
1989 only compatible with :mdp-value:`awh1-growth=linear`, since for
1990 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
1992 .. mdp:: awh1-target-beta-scaling
1995 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
1996 it is the unitless beta scaling factor taking values in (0,1).
1998 .. mdp:: awh1-target-cutoff
2001 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2003 .. mdp:: awh1-user-data
2007 Initialize the PMF and target distribution with default values.
2011 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2012 :ref:`gmx mdrun` will expect a file ``awh-init.xvg`` to be present in the run directory.
2013 For multiple biases, :ref:`gmx mdrun` expects files ``awh-init1.xvg``, ``awh-init2.xvg``, etc.
2014 The file name can be changed with the ``-awh`` option.
2015 The first :mdp:`awh1-ndim` columns of
2016 each input file should contain the coordinate values, such that each row defines a point in
2017 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
2018 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2019 be in the same column as written by :ref:`gmx awh`.
2021 .. mdp:: awh1-share-group
2025 Do not share the bias.
2027 .. mdp-value:: positive
2029 Share the bias and PMF estimates within and/or between simulations.
2030 Within a simulation, the bias will be shared between biases that have the
2031 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2032 With :mdp-value:`awh-share-multisim=yes` and
2033 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2034 Sharing may increase convergence initially, although the starting configurations
2035 can be critical, especially when sharing between many biases.
2036 Currently, positive group values should start at 1 and increase
2037 by 1 for each subsequent bias that is shared.
2042 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2043 The following options should be specified for each such dimension. Below only
2044 the options for dimension number 1 is shown. Options for other dimension indices are
2045 obtained by replacing '1' by the dimension index.
2047 .. mdp:: awh1-dim1-coord-provider
2051 The module providing the reaction coordinate for this dimension.
2052 Currently AWH can only act on pull coordinates.
2054 .. mdp:: awh1-dim1-coord-index
2057 Index of the pull coordinate defining this coordinate dimension.
2059 .. mdp:: awh1-dim1-force-constant
2061 (0) \[kJ/mol/nm^2\] or \[kJ/mol/rad^2\]
2062 Force constant for the (convolved) umbrella potential(s) along this
2063 coordinate dimension.
2065 .. mdp:: awh1-dim1-start
2067 (0.0) \[nm\]/\[rad\]
2068 Start value of the sampling interval along this dimension. The range of allowed
2069 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2070 For periodic geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2071 is allowed. The interval will then wrap around from +period/2 to -period/2.
2073 .. mdp:: awh1-dim1-end
2075 (0.0) \[nm\]/\[rad\]
2076 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2078 .. mdp:: awh1-dim1-period
2080 (0.0) \[nm\]/\[rad\]
2081 The period of this reaction coordinate, use 0 when the coordinate is not periodic.
2083 .. mdp:: awh1-dim1-diffusion
2085 (1e-5) \[nm^2/ps\]/\[rad^2/ps\]
2086 Estimated diffusion constant for this coordinate dimension determining the initial
2087 biasing rate. This needs only be a rough estimate and should not critically
2088 affect the results unless it is set to something very low, leading to slow convergence,
2089 or very high, forcing the system far from equilibrium. Not setting this value
2090 explicitly generates a warning.
2092 .. mdp:: awh1-dim1-cover-diameter
2094 (0.0)) \[nm\]/\[rad\]
2095 Diameter that needs to be sampled by a single simulation around a coordinate value
2096 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2097 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2098 across each coordinate value.
2099 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2100 (:mdp:`awh1-share-group`>0).
2101 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2102 for many sharing simulations does not guarantee transitions across free energy barriers.
2103 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2104 has independently sampled the whole interval.
2109 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2110 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2111 that can be used to achieve such a rotation.
2117 No enforced rotation will be applied. All enforced rotation options will
2118 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2123 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2124 under the :mdp:`rot-group0` option.
2126 .. mdp:: rot-ngroups
2129 Number of rotation groups.
2133 Name of rotation group 0 in the index file.
2138 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2139 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2140 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2145 Use mass weighted rotation group positions.
2150 Rotation vector, will get normalized.
2155 Pivot point (nm) for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2160 Reference rotation rate (degree/ps) of group 0.
2165 Force constant (kJ/(mol*nm^2)) for group 0.
2167 .. mdp:: rot-slab-dist0
2170 Slab distance (nm), if a flexible axis rotation type was chosen.
2172 .. mdp:: rot-min-gauss0
2175 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2176 (for the flexible axis potentials).
2181 Value of additive constant epsilon' (nm^2) for ``rm2*`` and ``flex2*`` potentials.
2183 .. mdp:: rot-fit-method0
2186 Fitting method when determining the actual angle of a rotation group
2187 (can be one of ``rmsd``, ``norm``, or ``potential``).
2189 .. mdp:: rot-potfit-nsteps0
2192 For fit type ``potential``, the number of angular positions around the reference angle for which the
2193 rotation potential is evaluated.
2195 .. mdp:: rot-potfit-step0
2198 For fit type ``potential``, the distance in degrees between two angular positions.
2200 .. mdp:: rot-nstrout
2203 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2204 and the rotation potential energy.
2206 .. mdp:: rot-nstsout
2209 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2219 ignore distance restraint information in topology file
2221 .. mdp-value:: simple
2223 simple (per-molecule) distance restraints.
2225 .. mdp-value:: ensemble
2227 distance restraints over an ensemble of molecules in one
2228 simulation box. Normally, one would perform ensemble averaging
2229 over multiple subsystems, each in a separate box, using ``mdrun
2230 -multi``. Supply ``topol0.tpr``, ``topol1.tpr``, ... with
2231 different coordinates and/or velocities. The environment
2232 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2233 within each ensemble (usually equal to the ``mdrun -multi``
2236 .. mdp:: disre-weighting
2238 .. mdp-value:: equal
2240 divide the restraint force equally over all atom pairs in the
2243 .. mdp-value:: conservative
2245 the forces are the derivative of the restraint potential, this
2246 results in an weighting of the atom pairs to the reciprocal
2247 seventh power of the displacement. The forces are conservative
2248 when :mdp:`disre-tau` is zero.
2250 .. mdp:: disre-mixed
2254 the violation used in the calculation of the restraint force is
2255 the time-averaged violation
2259 the violation used in the calculation of the restraint force is
2260 the square root of the product of the time-averaged violation
2261 and the instantaneous violation
2265 (1000) \[kJ mol-1 nm-2\]
2266 force constant for distance restraints, which is multiplied by a
2267 (possibly) different factor for each restraint given in the `fac`
2268 column of the interaction in the topology file.
2273 time constant for distance restraints running average. A value of
2274 zero turns off time averaging.
2276 .. mdp:: nstdisreout
2279 period between steps when the running time-averaged and
2280 instantaneous distances of all atom pairs involved in restraints
2281 are written to the energy file (can make the energy file very
2288 ignore orientation restraint information in topology file
2292 use orientation restraints, ensemble averaging can be performed
2298 force constant for orientation restraints, which is multiplied by a
2299 (possibly) different weight factor for each restraint, can be set
2300 to zero to obtain the orientations from a free simulation
2305 time constant for orientation restraints running average. A value
2306 of zero turns off time averaging.
2308 .. mdp:: orire-fitgrp
2310 fit group for orientation restraining. This group of atoms is used
2311 to determine the rotation **R** of the system with respect to the
2312 reference orientation. The reference orientation is the starting
2313 conformation of the first subsystem. For a protein, backbone is a
2316 .. mdp:: nstorireout
2319 period between steps when the running time-averaged and
2320 instantaneous orientations for all restraints, and the molecular
2321 order tensor are written to the energy file (can make the energy
2325 Free energy calculations
2326 ^^^^^^^^^^^^^^^^^^^^^^^^
2328 .. mdp:: free-energy
2332 Only use topology A.
2336 Interpolate between topology A (lambda=0) to topology B
2337 (lambda=1) and write the derivative of the Hamiltonian with
2338 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2339 or the Hamiltonian differences with respect to other lambda
2340 values (as specified with foreign lambda) to the energy file
2341 and/or to ``dhdl.xvg``, where they can be processed by, for
2342 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2343 are interpolated linearly as described in the manual. When
2344 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2345 used for the LJ and Coulomb interactions.
2349 Turns on expanded ensemble simulation, where the alchemical state
2350 becomes a dynamic variable, allowing jumping between different
2351 Hamiltonians. See the expanded ensemble options for controlling how
2352 expanded ensemble simulations are performed. The different
2353 Hamiltonians used in expanded ensemble simulations are defined by
2354 the other free energy options.
2356 .. mdp:: init-lambda
2359 starting value for lambda (float). Generally, this should only be
2360 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2361 other cases, :mdp:`init-lambda-state` should be specified
2362 instead. Must be greater than or equal to 0.
2364 .. mdp:: delta-lambda
2367 increment per time step for lambda
2369 .. mdp:: init-lambda-state
2372 starting value for the lambda state (integer). Specifies which
2373 columm of the lambda vector (:mdp:`coul-lambdas`,
2374 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2375 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2376 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2377 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2378 the first column, and so on.
2380 .. mdp:: fep-lambdas
2383 Zero, one or more lambda values for which Delta H values will be
2384 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2385 steps. Values must be between 0 and 1. Free energy differences
2386 between different lambda values can then be determined with
2387 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2388 other -lambdas keywords because all components of the lambda vector
2389 that are not specified will use :mdp:`fep-lambdas` (including
2390 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2392 .. mdp:: coul-lambdas
2395 Zero, one or more lambda values for which Delta H values will be
2396 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2397 steps. Values must be between 0 and 1. Only the electrostatic
2398 interactions are controlled with this component of the lambda
2399 vector (and only if the lambda=0 and lambda=1 states have differing
2400 electrostatic interactions).
2402 .. mdp:: vdw-lambdas
2405 Zero, one or more lambda values for which Delta H values will be
2406 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2407 steps. Values must be between 0 and 1. Only the van der Waals
2408 interactions are controlled with this component of the lambda
2411 .. mdp:: bonded-lambdas
2414 Zero, one or more lambda values for which Delta H values will be
2415 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2416 steps. Values must be between 0 and 1. Only the bonded interactions
2417 are controlled with this component of the lambda vector.
2419 .. mdp:: restraint-lambdas
2422 Zero, one or more lambda values for which Delta H values will be
2423 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2424 steps. Values must be between 0 and 1. Only the restraint
2425 interactions: dihedral restraints, and the pull code restraints are
2426 controlled with this component of the lambda vector.
2428 .. mdp:: mass-lambdas
2431 Zero, one or more lambda values for which Delta H values will be
2432 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2433 steps. Values must be between 0 and 1. Only the particle masses are
2434 controlled with this component of the lambda vector.
2436 .. mdp:: temperature-lambdas
2439 Zero, one or more lambda values for which Delta H values will be
2440 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2441 steps. Values must be between 0 and 1. Only the temperatures
2442 controlled with this component of the lambda vector. Note that
2443 these lambdas should not be used for replica exchange, only for
2444 simulated tempering.
2446 .. mdp:: calc-lambda-neighbors
2449 Controls the number of lambda values for which Delta H values will
2450 be calculated and written out, if :mdp:`init-lambda-state` has
2451 been set. A positive value will limit the number of lambda points
2452 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2453 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2454 has a value of 2, energies for lambda points 3-7 will be calculated
2455 and writen out. A value of -1 means all lambda points will be
2456 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2457 1 is sufficient, while for MBAR -1 should be used.
2462 the soft-core alpha parameter, a value of 0 results in linear
2463 interpolation of the LJ and Coulomb interactions
2468 the power of the radial term in the soft-core equation. Possible
2469 values are 6 and 48. 6 is more standard, and is the default. When
2470 48 is used, then sc-alpha should generally be much lower (between
2476 Whether to apply the soft-core free energy interaction
2477 transformation to the Columbic interaction of a molecule. Default
2478 is no, as it is generally more efficient to turn off the Coulomic
2479 interactions linearly before turning off the van der Waals
2480 interactions. Note that it is only taken into account when lambda
2481 states are used, not with :mdp:`couple-lambda0` /
2482 :mdp:`couple-lambda1`, and you can still turn off soft-core
2483 interactions by setting :mdp:`sc-alpha` to 0.
2488 the power for lambda in the soft-core function, only the values 1
2494 the soft-core sigma for particles which have a C6 or C12 parameter
2495 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2497 .. mdp:: couple-moltype
2499 Here one can supply a molecule type (as defined in the topology)
2500 for calculating solvation or coupling free energies. There is a
2501 special option ``system`` that couples all molecule types in the
2502 system. This can be useful for equilibrating a system starting from
2503 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2504 on. The Van der Waals interactions and/or charges in this molecule
2505 type can be turned on or off between lambda=0 and lambda=1,
2506 depending on the settings of :mdp:`couple-lambda0` and
2507 :mdp:`couple-lambda1`. If you want to decouple one of several
2508 copies of a molecule, you need to copy and rename the molecule
2509 definition in the topology.
2511 .. mdp:: couple-lambda0
2513 .. mdp-value:: vdw-q
2515 all interactions are on at lambda=0
2519 the charges are zero (no Coulomb interactions) at lambda=0
2523 the Van der Waals interactions are turned at lambda=0; soft-core
2524 interactions will be required to avoid singularities
2528 the Van der Waals interactions are turned off and the charges
2529 are zero at lambda=0; soft-core interactions will be required to
2530 avoid singularities.
2532 .. mdp:: couple-lambda1
2534 analogous to :mdp:`couple-lambda1`, but for lambda=1
2536 .. mdp:: couple-intramol
2540 All intra-molecular non-bonded interactions for moleculetype
2541 :mdp:`couple-moltype` are replaced by exclusions and explicit
2542 pair interactions. In this manner the decoupled state of the
2543 molecule corresponds to the proper vacuum state without
2544 periodicity effects.
2548 The intra-molecular Van der Waals and Coulomb interactions are
2549 also turned on/off. This can be useful for partitioning
2550 free-energies of relatively large molecules, where the
2551 intra-molecular non-bonded interactions might lead to
2552 kinetically trapped vacuum conformations. The 1-4 pair
2553 interactions are not turned off.
2558 the frequency for writing dH/dlambda and possibly Delta H to
2559 dhdl.xvg, 0 means no ouput, should be a multiple of
2560 :mdp:`nstcalcenergy`.
2562 .. mdp:: dhdl-derivatives
2566 If yes (the default), the derivatives of the Hamiltonian with
2567 respect to lambda at each :mdp:`nstdhdl` step are written
2568 out. These values are needed for interpolation of linear energy
2569 differences with :ref:`gmx bar` (although the same can also be
2570 achieved with the right foreign lambda setting, that may not be as
2571 flexible), or with thermodynamic integration
2573 .. mdp:: dhdl-print-energy
2577 Include either the total or the potential energy in the dhdl
2578 file. Options are 'no', 'potential', or 'total'. This information
2579 is needed for later free energy analysis if the states of interest
2580 are at different temperatures. If all states are at the same
2581 temperature, this information is not needed. 'potential' is useful
2582 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2583 file. When rerunning from an existing trajectory, the kinetic
2584 energy will often not be correct, and thus one must compute the
2585 residual free energy from the potential alone, with the kinetic
2586 energy component computed analytically.
2588 .. mdp:: separate-dhdl-file
2592 The free energy values that are calculated (as specified with
2593 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2594 written out to a separate file, with the default name
2595 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2600 The free energy values are written out to the energy output file
2601 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2602 steps), where they can be extracted with :ref:`gmx energy` or
2603 used directly with :ref:`gmx bar`.
2605 .. mdp:: dh-hist-size
2608 If nonzero, specifies the size of the histogram into which the
2609 Delta H values (specified with foreign lambda) and the derivative
2610 dH/dl values are binned, and written to ener.edr. This can be used
2611 to save disk space while calculating free energy differences. One
2612 histogram gets written for each foreign lambda and two for the
2613 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2614 histogram settings (too small size or too wide bins) can introduce
2615 errors. Do not use histograms unless you're certain you need it.
2617 .. mdp:: dh-hist-spacing
2620 Specifies the bin width of the histograms, in energy units. Used in
2621 conjunction with :mdp:`dh-hist-size`. This size limits the
2622 accuracy with which free energies can be calculated. Do not use
2623 histograms unless you're certain you need it.
2626 Expanded Ensemble calculations
2627 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2629 .. mdp:: nstexpanded
2631 The number of integration steps beween attempted moves changing the
2632 system Hamiltonian in expanded ensemble simulations. Must be a
2633 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2640 No Monte Carlo in state space is performed.
2642 .. mdp-value:: metropolis-transition
2644 Uses the Metropolis weights to update the expanded ensemble
2645 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2648 .. mdp-value:: barker-transition
2650 Uses the Barker transition critera to update the expanded
2651 ensemble weight of each state i, defined by exp(-beta_new
2652 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2654 .. mdp-value:: wang-landau
2656 Uses the Wang-Landau algorithm (in state space, not energy
2657 space) to update the expanded ensemble weights.
2659 .. mdp-value:: min-variance
2661 Uses the minimum variance updating method of Escobedo et al. to
2662 update the expanded ensemble weights. Weights will not be the
2663 free energies, but will rather emphasize states that need more
2664 sampling to give even uncertainty.
2666 .. mdp:: lmc-mc-move
2670 No Monte Carlo in state space is performed.
2672 .. mdp-value:: metropolis-transition
2674 Randomly chooses a new state up or down, then uses the
2675 Metropolis critera to decide whether to accept or reject:
2676 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2678 .. mdp-value:: barker-transition
2680 Randomly chooses a new state up or down, then uses the Barker
2681 transition critera to decide whether to accept or reject:
2682 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2684 .. mdp-value:: gibbs
2686 Uses the conditional weights of the state given the coordinate
2687 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2690 .. mdp-value:: metropolized-gibbs
2692 Uses the conditional weights of the state given the coordinate
2693 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2694 to move to, EXCLUDING the current state, then uses a rejection
2695 step to ensure detailed balance. Always more efficient that
2696 Gibbs, though only marginally so in many situations, such as
2697 when only the nearest neighbors have decent phase space
2703 random seed to use for Monte Carlo moves in state space. When
2704 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2706 .. mdp:: mc-temperature
2708 Temperature used for acceptance/rejection for Monte Carlo moves. If
2709 not specified, the temperature of the simulation specified in the
2710 first group of :mdp:`ref-t` is used.
2715 The cutoff for the histogram of state occupancies to be reset, and
2716 the free energy incrementor to be changed from delta to delta *
2717 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2718 each histogram) / (average number of samples at each
2719 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2720 histogram is only considered flat if all Nratio > 0.8 AND
2721 simultaneously all 1/Nratio > 0.8.
2726 Each time the histogram is considered flat, then the current value
2727 of the Wang-Landau incrementor for the free energies is multiplied
2728 by :mdp:`wl-scale`. Value must be between 0 and 1.
2730 .. mdp:: init-wl-delta
2733 The initial value of the Wang-Landau incrementor in kT. Some value
2734 near 1 kT is usually most efficient, though sometimes a value of
2735 2-3 in units of kT works better if the free energy differences are
2738 .. mdp:: wl-oneovert
2741 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2742 the large sample limit. There is significant evidence that the
2743 standard Wang-Landau algorithms in state space presented here
2744 result in free energies getting 'burned in' to incorrect values
2745 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2746 then when the incrementor becomes less than 1/N, where N is the
2747 mumber of samples collected (and thus proportional to the data
2748 collection time, hence '1 over t'), then the Wang-Lambda
2749 incrementor is set to 1/N, decreasing every step. Once this occurs,
2750 :mdp:`wl-ratio` is ignored, but the weights will still stop
2751 updating when the equilibration criteria set in
2752 :mdp:`lmc-weights-equil` is achieved.
2754 .. mdp:: lmc-repeats
2757 Controls the number of times that each Monte Carlo swap type is
2758 performed each iteration. In the limit of large numbers of Monte
2759 Carlo repeats, then all methods converge to Gibbs sampling. The
2760 value will generally not need to be different from 1.
2762 .. mdp:: lmc-gibbsdelta
2765 Limit Gibbs sampling to selected numbers of neighboring states. For
2766 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2767 sampling over all of the states that are defined. A positive value
2768 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2769 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2770 value of -1 means that all states are considered. For less than 100
2771 states, it is probably not that expensive to include all states.
2773 .. mdp:: lmc-forced-nstart
2776 Force initial state space sampling to generate weights. In order to
2777 come up with reasonable initial weights, this setting allows the
2778 simulation to drive from the initial to the final lambda state,
2779 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2780 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2781 sufficiently long (thousands of steps, perhaps), then the weights
2782 will be close to correct. However, in most cases, it is probably
2783 better to simply run the standard weight equilibration algorithms.
2785 .. mdp:: nst-transition-matrix
2788 Frequency of outputting the expanded ensemble transition matrix. A
2789 negative number means it will only be printed at the end of the
2792 .. mdp:: symmetrized-transition-matrix
2795 Whether to symmetrize the empirical transition matrix. In the
2796 infinite limit the matrix will be symmetric, but will diverge with
2797 statistical noise for short timescales. Forced symmetrization, by
2798 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2799 like the existence of (small magnitude) negative eigenvalues.
2801 .. mdp:: mininum-var-min
2804 The min-variance strategy (option of :mdp:`lmc-stats` is only
2805 valid for larger number of samples, and can get stuck if too few
2806 samples are used at each state. :mdp:`mininum-var-min` is the
2807 minimum number of samples that each state that are allowed before
2808 the min-variance strategy is activated if selected.
2810 .. mdp:: init-lambda-weights
2812 The initial weights (free energies) used for the expanded ensemble
2813 states. Default is a vector of zero weights. format is similar to
2814 the lambda vector settings in :mdp:`fep-lambdas`, except the
2815 weights can be any floating point number. Units are kT. Its length
2816 must match the lambda vector lengths.
2818 .. mdp:: lmc-weights-equil
2822 Expanded ensemble weights continue to be updated throughout the
2827 The input expanded ensemble weights are treated as equilibrated,
2828 and are not updated throughout the simulation.
2830 .. mdp-value:: wl-delta
2832 Expanded ensemble weight updating is stopped when the
2833 Wang-Landau incrementor falls below this value.
2835 .. mdp-value:: number-all-lambda
2837 Expanded ensemble weight updating is stopped when the number of
2838 samples at all of the lambda states is greater than this value.
2840 .. mdp-value:: number-steps
2842 Expanded ensemble weight updating is stopped when the number of
2843 steps is greater than the level specified by this value.
2845 .. mdp-value:: number-samples
2847 Expanded ensemble weight updating is stopped when the number of
2848 total samples across all lambda states is greater than the level
2849 specified by this value.
2851 .. mdp-value:: count-ratio
2853 Expanded ensemble weight updating is stopped when the ratio of
2854 samples at the least sampled lambda state and most sampled
2855 lambda state greater than this value.
2857 .. mdp:: simulated-tempering
2860 Turn simulated tempering on or off. Simulated tempering is
2861 implemented as expanded ensemble sampling with different
2862 temperatures instead of different Hamiltonians.
2864 .. mdp:: sim-temp-low
2867 Low temperature for simulated tempering.
2869 .. mdp:: sim-temp-high
2872 High temperature for simulated tempering.
2874 .. mdp:: simulated-tempering-scaling
2876 Controls the way that the temperatures at intermediate lambdas are
2877 calculated from the :mdp:`temperature-lambdas` part of the lambda
2880 .. mdp-value:: linear
2882 Linearly interpolates the temperatures using the values of
2883 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2884 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2885 a temperature of 350. A nonlinear set of temperatures can always
2886 be implemented with uneven spacing in lambda.
2888 .. mdp-value:: geometric
2890 Interpolates temperatures geometrically between
2891 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2892 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2893 :mdp:`sim-temp-low`) raised to the power of
2894 (i/(ntemps-1)). This should give roughly equal exchange for
2895 constant heat capacity, though of course things simulations that
2896 involve protein folding have very high heat capacity peaks.
2898 .. mdp-value:: exponential
2900 Interpolates temperatures exponentially between
2901 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2902 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2903 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2904 (i))-1)/(exp(1.0)-i)).
2912 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2913 in groups Protein and Sol will experience constant acceleration as
2914 specified in the :mdp:`accelerate` line
2919 acceleration for :mdp:`acc-grps`; x, y and z for each group
2920 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2921 constant acceleration of 0.1 nm ps-2 in X direction, second group
2926 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2927 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2928 specifies for which dimension the freezing applies. To avoid
2929 spurious contibrutions to the virial and pressure due to large
2930 forces between completely frozen atoms you need to use energy group
2931 exclusions, this also saves computing time. Note that coordinates
2932 of frozen atoms are not scaled by pressure-coupling algorithms.
2936 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2937 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
2938 N N N N`` means that particles in the first group can move only in
2939 Z direction. The particles in the second group can move in any
2942 .. mdp:: cos-acceleration
2945 the amplitude of the acceleration profile for calculating the
2946 viscosity. The acceleration is in the X-direction and the magnitude
2947 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2948 added to the energy file: the amplitude of the velocity profile and
2953 (0 0 0 0 0 0) \[nm ps-1\]
2954 The velocities of deformation for the box elements: a(x) b(y) c(z)
2955 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2956 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2957 elements are corrected for periodicity. The coordinates are
2958 transformed accordingly. Frozen degrees of freedom are (purposely)
2959 also transformed. The time ts is set to t at the first step and at
2960 steps at which x and v are written to trajectory to ensure exact
2961 restarts. Deformation can be used together with semiisotropic or
2962 anisotropic pressure coupling when the appropriate
2963 compressibilities are set to zero. The diagonal elements can be
2964 used to strain a solid. The off-diagonal elements can be used to
2965 shear a solid or a liquid.
2969 .. mdp:: electric-field-x ; electric-field-y ; electric-field-z
2971 Here you can specify an electric field that optionally can be
2972 alternating and pulsed. The general expression for the field
2973 has the form of a gaussian laser pulse:
2975 E(t) = E0 exp ( -(t-t0)^2/(2 sigma^2) ) cos(omega (t-t0))
2977 For example, the four parameters for direction x are set in the
2978 three fields of :mdp:`electric-field-x` (and similar for y and z)
2981 electric-field-x = E0 omega t0 sigma
2983 In the special case that sigma = 0, the exponential term is omitted
2984 and only the cosine term is used. If also omega = 0 a static
2985 electric field is applied.
2987 More details in Carl Caleman and David van der Spoel: Picosecond
2988 Melting of Ice by an Infrared Laser Pulse - A Simulation Study
2989 Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008)
2993 Mixed quantum/classical molecular dynamics
2994 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3004 Do a QM/MM simulation. Several groups can be described at
3005 different QM levels separately. These are specified in the
3006 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
3007 initio* theory at which the groups are described is specified by
3008 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
3009 groups at different levels of theory is only possible with the
3010 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
3014 groups to be descibed at the QM level
3018 .. mdp-value:: normal
3020 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
3021 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
3022 *ab initio* theory. The rest of the system is described at the
3023 MM level. The QM and MM subsystems interact as follows: MM point
3024 charges are included in the QM one-electron hamiltonian and all
3025 Lennard-Jones interactions are described at the MM level.
3027 .. mdp-value:: ONIOM
3029 The interaction between the subsystem is described using the
3030 ONIOM method by Morokuma and co-workers. There can be more than
3031 one :mdp:`QMMM-grps` each modeled at a different level of QM
3032 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
3037 Method used to compute the energy and gradients on the QM
3038 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
3039 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
3040 included in the active space is specified by :mdp:`CASelectrons`
3041 and :mdp:`CASorbitals`.
3046 Basis set used to expand the electronic wavefuntion. Only Gaussian
3047 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3048 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
3053 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
3054 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
3055 layer needs to be specified separately.
3060 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
3061 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
3062 needs to be specified separately.
3064 .. mdp:: CASorbitals
3067 The number of orbitals to be included in the active space when
3068 doing a CASSCF computation.
3070 .. mdp:: CASelectrons
3073 The number of electrons to be included in the active space when
3074 doing a CASSCF computation.
3080 No surface hopping. The system is always in the electronic
3085 Do a QM/MM MD simulation on the excited state-potential energy
3086 surface and enforce a *diabatic* hop to the ground-state when
3087 the system hits the conical intersection hyperline in the course
3088 the simulation. This option only works in combination with the
3095 .. mdp:: implicit-solvent
3103 Do a simulation with implicit solvent using the Generalized Born
3104 formalism. Three different methods for calculating the Born
3105 radii are available, Still, HCT and OBC. These are specified
3106 with the :mdp:`gb-algorithm` field. The non-polar solvation is
3107 specified with the :mdp:`sa-algorithm` field.
3109 .. mdp:: gb-algorithm
3111 .. mdp-value:: Still
3113 Use the Still method to calculate the Born radii
3117 Use the Hawkins-Cramer-Truhlar method to calculate the Born
3122 Use the Onufriev-Bashford-Case method to calculate the Born
3128 Frequency to (re)-calculate the Born radii. For most practial
3129 purposes, setting a value larger than 1 violates energy
3130 conservation and leads to unstable trajectories.
3135 Cut-off for the calculation of the Born radii. Currently must be
3138 .. mdp:: gb-epsilon-solvent
3141 Dielectric constant for the implicit solvent
3143 .. mdp:: gb-saltconc
3146 Salt concentration for implicit solvent models, currently not used
3148 .. mdp:: gb-obc-alpha
3149 .. mdp:: gb-obc-beta
3150 .. mdp:: gb-obc-gamma
3152 Scale factors for the OBC model. Default values of 1, 0.78 and 4.85
3153 respectively are for OBC(II). Values for OBC(I) are 0.8, 0 and 2.91
3156 .. mdp:: gb-dielectric-offset
3159 Distance for the di-electric offset when calculating the Born
3160 radii. This is the offset between the center of each atom the
3161 center of the polarization energy for the corresponding atom
3163 .. mdp:: sa-algorithm
3165 .. mdp-value:: Ace-approximation
3167 Use an Ace-type approximation
3171 No non-polar solvation calculation done. For GBSA only the polar
3172 part gets calculated
3174 .. mdp:: sa-surface-tension
3177 Default value for surface tension with SA algorithms. The default
3178 value is -1; Note that if this default value is not changed it will
3179 be overridden by :ref:`gmx grompp` using values that are specific
3180 for the choice of radii algorithm (0.0049 kcal/mol/Angstrom^2 for
3181 Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will
3182 while using an sa-algorithm other than None means no non-polar
3183 calculations are done.
3186 Computational Electrophysiology
3187 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3188 Use these options to switch on and control ion/water position exchanges in "Computational
3189 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3195 Do not enable ion/water position exchanges.
3197 .. mdp-value:: X ; Y ; Z
3199 Allow for ion/water position exchanges along the chosen direction.
3200 In a typical setup with the membranes parallel to the x-y plane,
3201 ion/water pairs need to be exchanged in Z direction to sustain the
3202 requested ion concentrations in the compartments.
3204 .. mdp:: swap-frequency
3206 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3207 per compartment are determined and exchanges made if necessary.
3208 Normally it is not necessary to check at every time step.
3209 For typical Computational Electrophysiology setups, a value of about 100 is
3210 sufficient and yields a negligible performance impact.
3212 .. mdp:: split-group0
3214 Name of the index group of the membrane-embedded part of channel #0.
3215 The center of mass of these atoms defines one of the compartment boundaries
3216 and should be chosen such that it is near the center of the membrane.
3218 .. mdp:: split-group1
3220 Channel #1 defines the position of the other compartment boundary.
3222 .. mdp:: massw-split0
3224 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3228 Use the geometrical center.
3232 Use the center of mass.
3234 .. mdp:: massw-split1
3236 (no) As above, but for split-group #1.
3238 .. mdp:: solvent-group
3240 Name of the index group of solvent molecules.
3242 .. mdp:: coupl-steps
3244 (\10) Average the number of ions per compartment over these many swap attempt steps.
3245 This can be used to prevent that ions near a compartment boundary
3246 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3250 (1) The number of different ion types to be controlled. These are during the
3251 simulation exchanged with solvent molecules to reach the desired reference numbers.
3253 .. mdp:: iontype0-name
3255 Name of the first ion type.
3257 .. mdp:: iontype0-in-A
3259 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3260 The default value of -1 means: use the number of ions as found in time step 0
3263 .. mdp:: iontype0-in-B
3265 (-1) Reference number of ions of type 0 for compartment B.
3267 .. mdp:: bulk-offsetA
3269 (0.0) Offset of the first swap layer from the compartment A midplane.
3270 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3271 at maximum distance (= bulk concentration) to the split group layers. However,
3272 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3273 towards one of the compartment-partitioning layers (at +/- 1.0).
3275 .. mdp:: bulk-offsetB
3277 (0.0) Offset of the other swap layer from the compartment B midplane.
3282 (\1) Only swap ions if threshold difference to requested count is reached.
3286 (2.0) \[nm\] Radius of the split cylinder #0.
3287 Two split cylinders (mimicking the channel pores) can optionally be defined
3288 relative to the center of the split group. With the help of these cylinders
3289 it can be counted which ions have passed which channel. The split cylinder
3290 definition has no impact on whether or not ion/water swaps are done.
3294 (1.0) \[nm\] Upper extension of the split cylinder #0.
3298 (1.0) \[nm\] Lower extension of the split cylinder #0.
3302 (2.0) \[nm\] Radius of the split cylinder #1.
3306 (1.0) \[nm\] Upper extension of the split cylinder #1.
3310 (1.0) \[nm\] Lower extension of the split cylinder #1.
3313 User defined thingies
3314 ^^^^^^^^^^^^^^^^^^^^^
3318 .. mdp:: userint1 (0)
3319 .. mdp:: userint2 (0)
3320 .. mdp:: userint3 (0)
3321 .. mdp:: userint4 (0)
3322 .. mdp:: userreal1 (0)
3323 .. mdp:: userreal2 (0)
3324 .. mdp:: userreal3 (0)
3325 .. mdp:: userreal4 (0)
3327 These you can use if you modify code. You can pass integers and
3328 reals and groups to your subroutine. Check the inputrec definition
3329 in ``src/gromacs/mdtypes/inputrec.h``
3334 This feature has been removed from |Gromacs|, but so that old
3335 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3336 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3337 fatal error if this is set.
3343 .. _reference manual: gmx-manual-parent-dir_