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 pair list. Since pair list 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 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
233 .. mdp-value:: Linear-acceleration-correction
235 Remove center of mass translational velocity. Correct the center of
236 mass position assuming linear acceleration over :mdp:`nstcomm` steps.
237 This is useful for cases where an acceleration is expected on the
238 center of mass which is nearly constant over :mdp:`nstcomm` steps.
239 This can occur for example when pulling on a group using an absolute
244 No restriction on the center of mass motion
249 frequency for center of mass motion removal
253 group(s) for center of mass motion removal, default is the whole
262 (0) [amu ps\ :sup:`-1`]
263 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
264 the friction coefficient for each particle is calculated as mass/
270 used to initialize random generator for thermal noise for
271 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
272 a pseudo random seed is used. When running BD or SD on multiple
273 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
274 the processor number.
282 (10.0) [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
283 the minimization is converged when the maximum force is smaller
294 frequency of performing 1 steepest descent step while doing
295 conjugate gradient energy minimization.
300 Number of correction steps to use for L-BFGS minimization. A higher
301 number is (at least theoretically) more accurate, but slower.
304 Shell Molecular Dynamics
305 ^^^^^^^^^^^^^^^^^^^^^^^^
307 When shells or flexible constraints are present in the system the
308 positions of the shells and the lengths of the flexible constraints
309 are optimized at every time step until either the RMS force on the
310 shells and constraints is less than :mdp:`emtol`, or a maximum number
311 of iterations :mdp:`niter` has been reached. Minimization is converged
312 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
313 value should be 1.0 at most.
318 maximum number of iterations for optimizing the shell positions and
319 the flexible constraints.
324 the step size for optimizing the flexible constraints. Should be
325 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
326 particles in a flexible constraint and d2V/dq2 is the second
327 derivative of the potential in the constraint direction. Hopefully
328 this number does not differ too much between the flexible
329 constraints, as the number of iterations and thus the runtime is
330 very sensitive to fcstep. Try several values!
333 Test particle insertion
334 ^^^^^^^^^^^^^^^^^^^^^^^
339 the test particle insertion radius, see integrators
340 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
349 number of steps that elapse between writing coordinates to the output
350 trajectory file (:ref:`trr`), the last coordinates are always written
355 number of steps that elapse between writing velocities to the output
356 trajectory file (:ref:`trr`), the last velocities are always written
361 number of steps that elapse between writing forces to the output
362 trajectory file (:ref:`trr`), the last forces are always written.
367 number of steps that elapse between writing energies to the log
368 file, the last energies are always written
370 .. mdp:: nstcalcenergy
373 number of steps that elapse between calculating the energies, 0 is
374 never. This option is only relevant with dynamics. This option affects the
375 performance in parallel simulations, because calculating energies
376 requires global communication between all processes which can
377 become a bottleneck at high parallelization.
382 number of steps that elapse between writing energies to energy file,
383 the last energies are always written, should be a multiple of
384 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
385 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
386 energy file, so :ref:`gmx energy` can report exact energy averages
387 and fluctuations also when :mdp:`nstenergy` > 1
389 .. mdp:: nstxout-compressed
392 number of steps that elapse between writing position coordinates
393 using lossy compression (:ref:`xtc` file)
395 .. mdp:: compressed-x-precision
398 precision with which to write to the compressed trajectory file
400 .. mdp:: compressed-x-grps
402 group(s) to write to the compressed trajectory file, by default the
403 whole system is written (if :mdp:`nstxout-compressed` > 0)
407 group(s) for which to write to write short-ranged non-bonded
408 potential energies to the energy file (not supported on GPUs)
414 .. mdp:: cutoff-scheme
416 .. mdp-value:: Verlet
418 Generate a pair list with buffering. The buffer size is
419 automatically set based on :mdp:`verlet-buffer-tolerance`,
420 unless this is set to -1, in which case :mdp:`rlist` will be
421 used. This option has an explicit, exact cut-off at :mdp:`rvdw`
422 equal to :mdp:`rcoulomb`, unless PME or Ewald is used, in which
423 case :mdp:`rcoulomb` > :mdp:`rvdw` is allowed. Currently only
424 cut-off, reaction-field, PME or Ewald electrostatics and plain
425 LJ are supported. Some :ref:`gmx mdrun` functionality is not yet
426 supported with the :mdp-value:`cutoff-scheme=Verlet` scheme, but :ref:`gmx grompp`
427 checks for this. Native GPU acceleration is only supported with
428 :mdp-value:`cutoff-scheme=Verlet`. With GPU-accelerated PME or with separate PME
429 ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
430 balance by scaling :mdp:`rcoulomb` and the grid spacing. This
431 can be turned off with ``mdrun -notunepme``. :mdp-value:`cutoff-scheme=Verlet` is
432 faster than :mdp-value:`cutoff-scheme=group` when there is no water, or if
433 :mdp-value:`cutoff-scheme=group` would use a pair-list buffer to conserve energy.
437 Generate a pair list for groups of atoms. These groups
438 correspond to the charge groups in the topology. This was the
439 only cut-off treatment scheme before version 4.6, and is
440 **deprecated since 5.1**. There is no explicit buffering of
441 the pair list. This enables efficient force calculations for
442 water, but energy is only conserved when a buffer is explicitly
451 Frequency to update the neighbor list. When this is 0, the
452 neighbor list is made only once. With energy minimization the
453 pair list will be updated for every energy evaluation when
454 :mdp:`nstlist` is greater than 0. With :mdp-value:`cutoff-scheme=Verlet` and
455 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
456 a minimum value and :ref:`gmx mdrun` might increase it, unless
457 it is set to 1. With parallel simulations and/or non-bonded
458 force calculation on the GPU, a value of 20 or 40 often gives
459 the best performance. With :mdp-value:`cutoff-scheme=group` and non-exact
460 cut-off's, :mdp:`nstlist` will affect the accuracy of your
461 simulation and it can not be chosen freely.
465 The neighbor list is only constructed once and never
466 updated. This is mainly useful for vacuum simulations in which
467 all particles see each other.
477 Make a grid in the box and only check atoms in neighboring grid
478 cells when constructing a new neighbor list every
479 :mdp:`nstlist` steps. In large systems grid search is much
480 faster than simple search.
482 .. mdp-value:: simple
484 Check every atom in the box when constructing a new neighbor
485 list every :mdp:`nstlist` steps (only with :mdp-value:`cutoff-scheme=group`
492 Use periodic boundary conditions in all directions.
496 Use no periodic boundary conditions, ignore the box. To simulate
497 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
498 best performance without cut-offs on a single MPI rank, set
499 :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`.
503 Use periodic boundary conditions in x and y directions
504 only. This works only with :mdp-value:`ns-type=grid` and can be used
505 in combination with walls_. Without walls or with only one wall
506 the system size is infinite in the z direction. Therefore
507 pressure coupling or Ewald summation methods can not be
508 used. These disadvantages do not apply when two walls are used.
510 .. mdp:: periodic-molecules
514 molecules are finite, fast molecular PBC can be used
518 for systems with molecules that couple to themselves through the
519 periodic boundary conditions, this requires a slower PBC
520 algorithm and molecules are not made whole in the output
522 .. mdp:: verlet-buffer-tolerance
524 (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
526 Useful only with the :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`. This sets
527 the maximum allowed error for pair interactions per particle caused
528 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
529 :mdp:`nstlist` and the Verlet buffer size are fixed (for
530 performance reasons), particle pairs not in the pair list can
531 occasionally get within the cut-off distance during
532 :mdp:`nstlist` -1 steps. This causes very small jumps in the
533 energy. In a constant-temperature ensemble, these very small energy
534 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
535 estimate assumes a homogeneous particle distribution, hence the
536 errors might be slightly underestimated for multi-phase
537 systems. (See the `reference manual`_ for details). For longer
538 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
539 overestimated, because the interactions between particles are
540 ignored. Combined with cancellation of errors, the actual drift of
541 the total energy is usually one to two orders of magnitude
542 smaller. Note that the generated buffer size takes into account
543 that the |Gromacs| pair-list setup leads to a reduction in the
544 drift by a factor 10, compared to a simple particle-pair based
545 list. Without dynamics (energy minimization etc.), the buffer is 5%
546 of the cut-off. For NVE simulations the initial temperature is
547 used, unless this is zero, in which case a buffer of 10% is
548 used. For NVE simulations the tolerance usually needs to be lowered
549 to achieve proper energy conservation on the nanosecond time
550 scale. To override the automated buffer setting, use
551 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
556 Cut-off distance for the short-range neighbor list. With the
557 :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`, this is by default set by the
558 :mdp:`verlet-buffer-tolerance` option and the value of
559 :mdp:`rlist` is ignored.
567 .. mdp-value:: Cut-off
569 Plain cut-off with pair list radius :mdp:`rlist` and
570 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
575 Classical Ewald sum electrostatics. The real-space cut-off
576 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
577 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
578 of wave vectors used in reciprocal space is controlled by
579 :mdp:`fourierspacing`. The relative accuracy of
580 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
582 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
583 large systems. It is included mainly for reference - in most
584 cases PME will perform much better.
588 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
589 space is similar to the Ewald sum, while the reciprocal part is
590 performed with FFTs. Grid dimensions are controlled with
591 :mdp:`fourierspacing` and the interpolation order with
592 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
593 interpolation the electrostatic forces have an accuracy of
594 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
595 this you might try 0.15 nm. When running in parallel the
596 interpolation parallelizes better than the FFT, so try
597 decreasing grid dimensions while increasing interpolation.
599 .. mdp-value:: P3M-AD
601 Particle-Particle Particle-Mesh algorithm with analytical
602 derivative for for long range electrostatic interactions. The
603 method and code is identical to SPME, except that the influence
604 function is optimized for the grid. This gives a slight increase
607 .. mdp-value:: Reaction-Field
609 Reaction field electrostatics with Coulomb cut-off
610 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
611 dielectric constant beyond the cut-off is
612 :mdp:`epsilon-rf`. The dielectric constant can be set to
613 infinity by setting :mdp:`epsilon-rf` =0.
615 .. mdp-value:: Generalized-Reaction-Field
617 Generalized reaction field with Coulomb cut-off
618 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rcoulomb`. The
619 dielectric constant beyond the cut-off is
620 :mdp:`epsilon-rf`. The ionic strength is computed from the
621 number of charged (*i.e.* with non zero charge) charge
622 groups. The temperature for the GRF potential is set with
625 .. mdp-value:: Reaction-Field-zero
627 In |Gromacs|, normal reaction-field electrostatics with
628 :mdp-value:`cutoff-scheme=group` leads to bad energy
629 conservation. :mdp-value:`coulombtype=Reaction-Field-zero` solves this by making
630 the potential zero beyond the cut-off. It can only be used with
631 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
632 only for that value the force vanishes at the
633 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
634 :mdp:`rcoulomb` to accommodate the size of charge groups
635 and diffusion between neighbor list updates. This, and the fact
636 that table lookups are used instead of analytical functions make
637 reaction-field-zero computationally more expensive than
638 normal reaction-field.
642 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
643 might want to use :mdp-value:`coulombtype=Reaction-Field-zero` instead, which has
644 a similar potential shape, but has a physical interpretation and
645 has better energies due to the exclusion correction terms.
647 .. mdp-value:: Encad-Shift
649 The Coulomb potential is decreased over the whole range, using
650 the definition from the Encad simulation package.
652 .. mdp-value:: Switch
654 Analogous to :mdp-value:`vdwtype=Switch` for
655 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
656 serious artifacts, advice: use :mdp-value:`coulombtype=Reaction-Field-zero`
661 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
662 with user-defined potential functions for repulsion, dispersion
663 and Coulomb. When pair interactions are present, :ref:`gmx
664 mdrun` also expects to find a file ``tablep.xvg`` for the pair
665 interactions. When the same interactions should be used for
666 non-bonded and pair interactions the user can specify the same
667 file name for both table files. These files should contain 7
668 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
669 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
670 function, ``g(x)`` the dispersion function and ``h(x)`` the
671 repulsion function. When :mdp:`vdwtype` is not set to User the
672 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
673 the non-bonded interactions ``x`` values should run from 0 to
674 the largest cut-off distance + :mdp:`table-extension` and
675 should be uniformly spaced. For the pair interactions the table
676 length in the file will be used. The optimal spacing, which is
677 used for non-user tables, is ``0.002 nm`` when you run in mixed
678 precision or ``0.0005 nm`` when you run in double precision. The
679 function value at ``x=0`` is not important. More information is
680 in the printed manual.
682 .. mdp-value:: PME-Switch
684 A combination of PME and a switch function for the direct-space
685 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
686 :mdp:`rlist`. This is mainly useful constant energy simulations
687 (note that using PME with :mdp-value:`cutoff-scheme=Verlet`
688 will be more efficient).
690 .. mdp-value:: PME-User
692 A combination of PME and user tables (see
693 above). :mdp:`rcoulomb` is allowed to be smaller than
694 :mdp:`rlist`. The PME mesh contribution is subtracted from the
695 user table by :ref:`gmx mdrun`. Because of this subtraction the
696 user tables should contain about 10 decimal places.
698 .. mdp-value:: PME-User-Switch
700 A combination of PME-User and a switching function (see
701 above). The switching function is applied to final
702 particle-particle interaction, *i.e.* both to the user supplied
703 function and the PME Mesh correction part.
705 .. mdp:: coulomb-modifier
707 .. mdp-value:: Potential-shift-Verlet
709 Selects Potential-shift with the Verlet cutoff-scheme, as it is
710 (nearly) free; selects None with the group cutoff-scheme.
712 .. mdp-value:: Potential-shift
714 Shift the Coulomb potential by a constant such that it is zero
715 at the cut-off. This makes the potential the integral of the
716 force. Note that this does not affect the forces or the
721 Use an unmodified Coulomb potential. With the group scheme this
722 means no exact cut-off is used, energies and forces are
723 calculated for all pairs in the pair list.
725 .. mdp:: rcoulomb-switch
728 where to start switching the Coulomb potential, only relevant
729 when force or potential switching is used
734 distance for the Coulomb cut-off
739 The relative dielectric constant. A value of 0 means infinity.
744 The relative dielectric constant of the reaction field. This
745 is only used with reaction-field electrostatics. A value of 0
754 .. mdp-value:: Cut-off
756 Plain cut-off with pair list radius :mdp:`rlist` and VdW
757 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
761 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
762 grid dimensions are controlled with :mdp:`fourierspacing` in
763 the same way as for electrostatics, and the interpolation order
764 is controlled with :mdp:`pme-order`. The relative accuracy of
765 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
766 and the specific combination rules that are to be used by the
767 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
771 This functionality is deprecated and replaced by using
772 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
773 The LJ (not Buckingham) potential is decreased over the whole range and
774 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
775 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
776 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
777 size of charge groups and diffusion between neighbor list
780 .. mdp-value:: Switch
782 This functionality is deprecated and replaced by using
783 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
784 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
785 which it is switched off to reach zero at :mdp:`rvdw`. Both the
786 potential and force functions are continuously smooth, but be
787 aware that all switch functions will give rise to a bulge
788 (increase) in the force (since we are switching the
789 potential). The neighbor search cut-off :mdp:`rlist` should be
790 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
791 size of charge groups and diffusion between neighbor list
794 .. mdp-value:: Encad-Shift
796 The LJ (not Buckingham) potential is decreased over the whole
797 range, using the definition from the Encad simulation package.
801 See user for :mdp:`coulombtype`. The function value at zero is
802 not important. When you want to use LJ correction, make sure
803 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
804 function. When :mdp:`coulombtype` is not set to User the values
805 for the ``f`` and ``-f'`` columns are ignored.
807 .. mdp:: vdw-modifier
809 .. mdp-value:: Potential-shift-Verlet
811 Selects Potential-shift with the Verlet cutoff-scheme, as it is
812 (nearly) free; selects None with the group cutoff-scheme.
814 .. mdp-value:: Potential-shift
816 Shift the Van der Waals potential by a constant such that it is
817 zero at the cut-off. This makes the potential the integral of
818 the force. Note that this does not affect the forces or the
823 Use an unmodified Van der Waals potential. With the group scheme
824 this means no exact cut-off is used, energies and forces are
825 calculated for all pairs in the pair list.
827 .. mdp-value:: Force-switch
829 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
830 and :mdp:`rvdw`. This shifts the potential shift over the whole
831 range and switches it to zero at the cut-off. Note that this is
832 more expensive to calculate than a plain cut-off and it is not
833 required for energy conservation, since Potential-shift
834 conserves energy just as well.
836 .. mdp-value:: Potential-switch
838 Smoothly switches the potential to zero between
839 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
840 articifically large forces in the switching region and is much
841 more expensive to calculate. This option should only be used if
842 the force field you are using requires this.
847 where to start switching the LJ force and possibly the potential,
848 only relevant when force or potential switching is used
853 distance for the LJ or Buckingham cut-off
859 don't apply any correction
861 .. mdp-value:: EnerPres
863 apply long range dispersion corrections for Energy and Pressure
867 apply long range dispersion corrections for Energy only
873 .. mdp:: table-extension
876 Extension of the non-bonded potential lookup tables beyond the
877 largest cut-off distance. The value should be large enough to
878 account for charge group sizes and the diffusion between
879 neighbor-list updates. Without user defined potential the same
880 table length is used for the lookup tables for the 1-4
881 interactions, which are always tabulated irrespective of the use of
882 tables for the non-bonded interactions. The value of
883 :mdp:`table-extension` in no way affects the values of
884 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
886 .. mdp:: energygrp-table
888 When user tables are used for electrostatics and/or VdW, here one
889 can give pairs of energy groups for which seperate user tables
890 should be used. The two energy groups will be appended to the table
891 file name, in order of their definition in :mdp:`energygrps`,
892 seperated by underscores. For example, if ``energygrps = Na Cl
893 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
894 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
895 normal ``table.xvg`` which will be used for all other energy group
902 .. mdp:: fourierspacing
905 For ordinary Ewald, the ratio of the box dimensions and the spacing
906 determines a lower bound for the number of wave vectors to use in
907 each (signed) direction. For PME and P3M, that ratio determines a
908 lower bound for the number of Fourier-space grid points that will
909 be used along that axis. In all cases, the number for each
910 direction can be overridden by entering a non-zero value for that
911 :mdp:`fourier-nx` direction. For optimizing the relative load of
912 the particle-particle interactions and the mesh part of PME, it is
913 useful to know that the accuracy of the electrostatics remains
914 nearly constant when the Coulomb cut-off and the PME grid spacing
915 are scaled by the same factor.
922 Highest magnitude of wave vectors in reciprocal space when using Ewald.
923 Grid size when using PME or P3M. These values override
924 :mdp:`fourierspacing` per direction. The best choice is powers of
925 2, 3, 5 and 7. Avoid large primes.
930 Interpolation order for PME. 4 equals cubic interpolation. You
931 might try 6/8/10 when running in parallel and simultaneously
932 decrease grid dimension.
937 The relative strength of the Ewald-shifted direct potential at
938 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
939 will give a more accurate direct sum, but then you need more wave
940 vectors for the reciprocal sum.
942 .. mdp:: ewald-rtol-lj
945 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
946 to control the relative strength of the dispersion potential at
947 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
948 electrostatic potential.
950 .. mdp:: lj-pme-comb-rule
953 The combination rules used to combine VdW-parameters in the
954 reciprocal part of LJ-PME. Geometric rules are much faster than
955 Lorentz-Berthelot and usually the recommended choice, even when the
956 rest of the force field uses the Lorentz-Berthelot rules.
958 .. mdp-value:: Geometric
960 Apply geometric combination rules
962 .. mdp-value:: Lorentz-Berthelot
964 Apply Lorentz-Berthelot combination rules
966 .. mdp:: ewald-geometry
970 The Ewald sum is performed in all three dimensions.
974 The reciprocal sum is still performed in 3D, but a force and
975 potential correction applied in the `z` dimension to produce a
976 pseudo-2D summation. If your system has a slab geometry in the
977 `x-y` plane you can try to increase the `z`-dimension of the box
978 (a box height of 3 times the slab height is usually ok) and use
981 .. mdp:: epsilon-surface
984 This controls the dipole correction to the Ewald summation in
985 3D. The default value of zero means it is turned off. Turn it on by
986 setting it to the value of the relative permittivity of the
987 imaginary surface around your infinite system. Be careful - you
988 shouldn't use this if you have free mobile charges in your
989 system. This value does not affect the slab 3DC variant of the long
1000 No temperature coupling.
1002 .. mdp-value:: berendsen
1004 Temperature coupling with a Berendsen thermostat to a bath with
1005 temperature :mdp:`ref-t`, with time constant
1006 :mdp:`tau-t`. Several groups can be coupled separately, these
1007 are specified in the :mdp:`tc-grps` field separated by spaces.
1009 .. mdp-value:: nose-hoover
1011 Temperature coupling using a Nose-Hoover extended ensemble. The
1012 reference temperature and coupling groups are selected as above,
1013 but in this case :mdp:`tau-t` controls the period of the
1014 temperature fluctuations at equilibrium, which is slightly
1015 different from a relaxation time. For NVT simulations the
1016 conserved energy quantity is written to the energy and log files.
1018 .. mdp-value:: andersen
1020 Temperature coupling by randomizing a fraction of the particle velocities
1021 at each timestep. Reference temperature and coupling groups are
1022 selected as above. :mdp:`tau-t` is the average time between
1023 randomization of each molecule. Inhibits particle dynamics
1024 somewhat, but little or no ergodicity issues. Currently only
1025 implemented with velocity Verlet, and not implemented with
1028 .. mdp-value:: andersen-massive
1030 Temperature coupling by randomizing velocities of all particles at
1031 infrequent timesteps. Reference temperature and coupling groups are
1032 selected as above. :mdp:`tau-t` is the time between
1033 randomization of all molecules. Inhibits particle dynamics
1034 somewhat, but little or no ergodicity issues. Currently only
1035 implemented with velocity Verlet.
1037 .. mdp-value:: v-rescale
1039 Temperature coupling using velocity rescaling with a stochastic
1040 term (JCP 126, 014101). This thermostat is similar to Berendsen
1041 coupling, with the same scaling using :mdp:`tau-t`, but the
1042 stochastic term ensures that a proper canonical ensemble is
1043 generated. The random seed is set with :mdp:`ld-seed`. This
1044 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1045 simulations the conserved energy quantity is written to the
1046 energy and log file.
1051 The frequency for coupling the temperature. The default value of -1
1052 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1053 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1054 Verlet integrators :mdp:`nsttcouple` is set to 1.
1056 .. mdp:: nh-chain-length
1059 The number of chained Nose-Hoover thermostats for velocity Verlet
1060 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1061 only supports 1. Data for the NH chain variables is not printed
1062 to the :ref:`edr` file by default, but can be turned on with the
1063 :mdp:`print-nose-hoover-chains` option.
1065 .. mdp:: print-nose-hoover-chain-variables
1069 Do not store Nose-Hoover chain variables in the energy file.
1073 Store all positions and velocities of the Nose-Hoover chain
1078 groups to couple to separate temperature baths
1083 time constant for coupling (one for each group in
1084 :mdp:`tc-grps`), -1 means no temperature coupling
1089 reference temperature for coupling (one for each group in
1100 No pressure coupling. This means a fixed box size.
1102 .. mdp-value:: Berendsen
1104 Exponential relaxation pressure coupling with time constant
1105 :mdp:`tau-p`. The box is scaled every timestep. It has been
1106 argued that this does not yield a correct thermodynamic
1107 ensemble, but it is the most efficient way to scale a box at the
1110 .. mdp-value:: Parrinello-Rahman
1112 Extended-ensemble pressure coupling where the box vectors are
1113 subject to an equation of motion. The equation of motion for the
1114 atoms is coupled to this. No instantaneous scaling takes
1115 place. As for Nose-Hoover temperature coupling the time constant
1116 :mdp:`tau-p` is the period of pressure fluctuations at
1117 equilibrium. This is probably a better method when you want to
1118 apply pressure scaling during data collection, but beware that
1119 you can get very large oscillations if you are starting from a
1120 different pressure. For simulations where the exact fluctations
1121 of the NPT ensemble are important, or if the pressure coupling
1122 time is very short it may not be appropriate, as the previous
1123 time step pressure is used in some steps of the |Gromacs|
1124 implementation for the current time step pressure.
1128 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1129 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1130 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1131 time constant :mdp:`tau-p` is the period of pressure
1132 fluctuations at equilibrium. This is probably a better method
1133 when you want to apply pressure scaling during data collection,
1134 but beware that you can get very large oscillations if you are
1135 starting from a different pressure. Currently (as of version
1136 5.1), it only supports isotropic scaling, and only works without
1141 Specifies the kind of isotropy of the pressure coupling used. Each
1142 kind takes one or more values for :mdp:`compressibility` and
1143 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1145 .. mdp-value:: isotropic
1147 Isotropic pressure coupling with time constant
1148 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1149 :mdp:`ref-p` is required.
1151 .. mdp-value:: semiisotropic
1153 Pressure coupling which is isotropic in the ``x`` and ``y``
1154 direction, but different in the ``z`` direction. This can be
1155 useful for membrane simulations. Two values each for
1156 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1157 ``x/y`` and ``z`` directions respectively.
1159 .. mdp-value:: anisotropic
1161 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1162 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1163 respectively. When the off-diagonal compressibilities are set to
1164 zero, a rectangular box will stay rectangular. Beware that
1165 anisotropic scaling can lead to extreme deformation of the
1168 .. mdp-value:: surface-tension
1170 Surface tension coupling for surfaces parallel to the
1171 xy-plane. Uses normal pressure coupling for the `z`-direction,
1172 while the surface tension is coupled to the `x/y` dimensions of
1173 the box. The first :mdp:`ref-p` value is the reference surface
1174 tension times the number of surfaces ``bar nm``, the second
1175 value is the reference `z`-pressure ``bar``. The two
1176 :mdp:`compressibility` values are the compressibility in the
1177 `x/y` and `z` direction respectively. The value for the
1178 `z`-compressibility should be reasonably accurate since it
1179 influences the convergence of the surface-tension, it can also
1180 be set to zero to have a box with constant height.
1185 The frequency for coupling the pressure. The default value of -1
1186 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1187 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1188 Verlet integrators :mdp:`nstpcouple` is set to 1.
1193 The time constant for pressure coupling (one value for all
1196 .. mdp:: compressibility
1199 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1200 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1201 required values is implied by :mdp:`pcoupltype`.
1206 The reference pressure for coupling. The number of required values
1207 is implied by :mdp:`pcoupltype`.
1209 .. mdp:: refcoord-scaling
1213 The reference coordinates for position restraints are not
1214 modified. Note that with this option the virial and pressure
1215 will depend on the absolute positions of the reference
1220 The reference coordinates are scaled with the scaling matrix of
1221 the pressure coupling.
1225 Scale the center of mass of the reference coordinates with the
1226 scaling matrix of the pressure coupling. The vectors of each
1227 reference coordinate to the center of mass are not scaled. Only
1228 one COM is used, even when there are multiple molecules with
1229 position restraints. For calculating the COM of the reference
1230 coordinates in the starting configuration, periodic boundary
1231 conditions are not taken into account.
1237 Simulated annealing is controlled separately for each temperature
1238 group in |Gromacs|. The reference temperature is a piecewise linear
1239 function, but you can use an arbitrary number of points for each
1240 group, and choose either a single sequence or a periodic behaviour for
1241 each group. The actual annealing is performed by dynamically changing
1242 the reference temperature used in the thermostat algorithm selected,
1243 so remember that the system will usually not instantaneously reach the
1244 reference temperature!
1248 Type of annealing for each temperature group
1252 No simulated annealing - just couple to reference temperature value.
1254 .. mdp-value:: single
1256 A single sequence of annealing points. If your simulation is
1257 longer than the time of the last point, the temperature will be
1258 coupled to this constant value after the annealing sequence has
1259 reached the last time point.
1261 .. mdp-value:: periodic
1263 The annealing will start over at the first reference point once
1264 the last reference time is reached. This is repeated until the
1267 .. mdp:: annealing-npoints
1269 A list with the number of annealing reference/control points used
1270 for each temperature group. Use 0 for groups that are not
1271 annealed. The number of entries should equal the number of
1274 .. mdp:: annealing-time
1276 List of times at the annealing reference/control points for each
1277 group. If you are using periodic annealing, the times will be used
1278 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1279 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1280 etc. The number of entries should equal the sum of the numbers
1281 given in :mdp:`annealing-npoints`.
1283 .. mdp:: annealing-temp
1285 List of temperatures at the annealing reference/control points for
1286 each group. The number of entries should equal the sum of the
1287 numbers given in :mdp:`annealing-npoints`.
1289 Confused? OK, let's use an example. Assume you have two temperature
1290 groups, set the group selections to ``annealing = single periodic``,
1291 the number of points of each group to ``annealing-npoints = 3 4``, the
1292 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1293 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1294 will be coupled to 298K at 0ps, but the reference temperature will
1295 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1296 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1297 second group is coupled to 298K at 0ps, it increases linearly to 320K
1298 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1299 decreases to 298K, and then it starts over with the same pattern
1300 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1301 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1311 Do not generate velocities. The velocities are set to zero
1312 when there are no velocities in the input structure file.
1316 Generate velocities in :ref:`gmx grompp` according to a
1317 Maxwell distribution at temperature :mdp:`gen-temp`, with
1318 random seed :mdp:`gen-seed`. This is only meaningful with
1319 :mdp-value:`integrator=md`.
1324 temperature for Maxwell distribution
1329 used to initialize random generator for random velocities,
1330 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1337 .. mdp:: constraints
1339 Controls which bonds in the topology will be converted to rigid
1340 holonomic constraints. Note that typical rigid water models do not
1341 have bonds, but rather a specialized ``[settles]`` directive, so
1342 are not affected by this keyword.
1346 No bonds converted to constraints.
1348 .. mdp-value:: h-bonds
1350 Convert the bonds with H-atoms to constraints.
1352 .. mdp-value:: all-bonds
1354 Convert all bonds to constraints.
1356 .. mdp-value:: h-angles
1358 Convert all bonds to constraints and convert the angles that
1359 involve H-atoms to bond-constraints.
1361 .. mdp-value:: all-angles
1363 Convert all bonds to constraints and all angles to bond-constraints.
1365 .. mdp:: constraint-algorithm
1367 Chooses which solver satisfies any non-SETTLE holonomic
1370 .. mdp-value:: LINCS
1372 LINear Constraint Solver. With domain decomposition the parallel
1373 version P-LINCS is used. The accuracy in set with
1374 :mdp:`lincs-order`, which sets the number of matrices in the
1375 expansion for the matrix inversion. After the matrix inversion
1376 correction the algorithm does an iterative correction to
1377 compensate for lengthening due to rotation. The number of such
1378 iterations can be controlled with :mdp:`lincs-iter`. The root
1379 mean square relative constraint deviation is printed to the log
1380 file every :mdp:`nstlog` steps. If a bond rotates more than
1381 :mdp:`lincs-warnangle` in one step, a warning will be printed
1382 both to the log file and to ``stderr``. LINCS should not be used
1383 with coupled angle constraints.
1385 .. mdp-value:: SHAKE
1387 SHAKE is slightly slower and less stable than LINCS, but does
1388 work with angle constraints. The relative tolerance is set with
1389 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1390 does not support constraints between atoms on different nodes,
1391 thus it can not be used with domain decompositon when inter
1392 charge-group constraints are present. SHAKE can not be used with
1393 energy minimization.
1395 .. mdp:: continuation
1397 This option was formerly known as ``unconstrained-start``.
1401 apply constraints to the start configuration and reset shells
1405 do not apply constraints to the start configuration and do not
1406 reset shells, useful for exact coninuation and reruns
1411 relative tolerance for SHAKE
1413 .. mdp:: lincs-order
1416 Highest order in the expansion of the constraint coupling
1417 matrix. When constraints form triangles, an additional expansion of
1418 the same order is applied on top of the normal expansion only for
1419 the couplings within such triangles. For "normal" MD simulations an
1420 order of 4 usually suffices, 6 is needed for large time-steps with
1421 virtual sites or BD. For accurate energy minimization an order of 8
1422 or more might be required. With domain decomposition, the cell size
1423 is limited by the distance spanned by :mdp:`lincs-order` +1
1424 constraints. When one wants to scale further than this limit, one
1425 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1426 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1427 )* :mdp:`lincs-order` remains constant.
1432 Number of iterations to correct for rotational lengthening in
1433 LINCS. For normal runs a single step is sufficient, but for NVE
1434 runs where you want to conserve energy accurately or for accurate
1435 energy minimization you might want to increase it to 2.
1437 .. mdp:: lincs-warnangle
1440 maximum angle that a bond can rotate before LINCS will complain
1446 bonds are represented by a harmonic potential
1450 bonds are represented by a Morse potential
1453 Energy group exclusions
1454 ^^^^^^^^^^^^^^^^^^^^^^^
1456 .. mdp:: energygrp-excl
1458 Pairs of energy groups for which all non-bonded interactions are
1459 excluded. An example: if you have two energy groups ``Protein`` and
1460 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1461 would give only the non-bonded interactions between the protein and
1462 the solvent. This is especially useful for speeding up energy
1463 calculations with ``mdrun -rerun`` and for excluding interactions
1464 within frozen groups.
1473 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1474 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1475 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1476 used (it is usually best to use semiisotropic pressure coupling
1477 with the ``x/y`` compressibility set to 0, as otherwise the surface
1478 area will change). Walls interact wit the rest of the system
1479 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1480 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1481 monitor the interaction of energy groups with each wall. The center
1482 of mass motion removal will be turned off in the ``z``-direction.
1484 .. mdp:: wall-atomtype
1486 the atom type name in the force field for each wall. By (for
1487 example) defining a special wall atom type in the topology with its
1488 own combination rules, this allows for independent tuning of the
1489 interaction of each atomtype with the walls.
1495 LJ integrated over the volume behind the wall: 9-3 potential
1499 LJ integrated over the wall surface: 10-4 potential
1503 direct LJ potential with the ``z`` distance from the wall
1507 user defined potentials indexed with the ``z`` distance from the
1508 wall, the tables are read analogously to the
1509 :mdp:`energygrp-table` option, where the first name is for a
1510 "normal" energy group and the second name is ``wall0`` or
1511 ``wall1``, only the dispersion and repulsion columns are used
1513 .. mdp:: wall-r-linpot
1516 Below this distance from the wall the potential is continued
1517 linearly and thus the force is constant. Setting this option to a
1518 postive value is especially useful for equilibration when some
1519 atoms are beyond a wall. When the value is <=0 (<0 for
1520 :mdp:`wall-type` =table), a fatal error is generated when atoms
1523 .. mdp:: wall-density
1525 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1526 the number density of the atoms for each wall for wall types 9-3
1529 .. mdp:: wall-ewald-zfac
1532 The scaling factor for the third box vector for Ewald summation
1533 only, the minimum is 2. Ewald summation can only be used with
1534 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1535 ``=3dc``. The empty layer in the box serves to decrease the
1536 unphysical Coulomb interaction between periodic images.
1542 Note that where pulling coordinates are applicable, there can be more
1543 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1544 variables will exist accordingly. Documentation references to things
1545 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1546 applicable pulling coordinate, eg. the second pull coordinate is described by
1547 pull-coord2-vec, pull-coord2-k, and so on.
1553 No center of mass pulling. All the following pull options will
1554 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1559 Center of mass pulling will be applied on 1 or more groups using
1560 1 or more pull coordinates.
1562 .. mdp:: pull-cylinder-r
1565 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1567 .. mdp:: pull-constr-tol
1570 the relative constraint tolerance for constraint pulling
1572 .. mdp:: pull-print-com
1576 do not print the COM for any group
1580 print the COM of all groups for all pull coordinates
1582 .. mdp:: pull-print-ref-value
1586 do not print the reference value for each pull coordinate
1590 print the reference value for each pull coordinate
1592 .. mdp:: pull-print-components
1596 only print the distance for each pull coordinate
1600 print the distance and Cartesian components selected in
1601 :mdp:`pull-coord1-dim`
1603 .. mdp:: pull-nstxout
1606 frequency for writing out the COMs of all the pull group (0 is
1609 .. mdp:: pull-nstfout
1612 frequency for writing out the force of all the pulled group
1616 .. mdp:: pull-ngroups
1619 The number of pull groups, not including the absolute reference
1620 group, when used. Pull groups can be reused in multiple pull
1621 coordinates. Below only the pull options for group 1 are given,
1622 further groups simply increase the group index number.
1624 .. mdp:: pull-ncoords
1627 The number of pull coordinates. Below only the pull options for
1628 coordinate 1 are given, further coordinates simply increase the
1629 coordinate index number.
1631 .. mdp:: pull-group1-name
1633 The name of the pull group, is looked up in the index file or in
1634 the default groups to obtain the atoms involved.
1636 .. mdp:: pull-group1-weights
1638 Optional relative weights which are multiplied with the masses of
1639 the atoms to give the total weight for the COM. The number should
1640 be 0, meaning all 1, or the number of atoms in the pull group.
1642 .. mdp:: pull-group1-pbcatom
1645 The reference atom for the treatment of periodic boundary
1646 conditions inside the group (this has no effect on the treatment of
1647 the pbc between groups). This option is only important when the
1648 diameter of the pull group is larger than half the shortest box
1649 vector. For determining the COM, all atoms in the group are put at
1650 their periodic image which is closest to
1651 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1652 atom (number wise) is used. This parameter is not used with
1653 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1654 weighting, which is useful for a group of molecules in a periodic
1655 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1658 .. mdp:: pull-coord1-type
1660 .. mdp-value:: umbrella
1662 Center of mass pulling using an umbrella potential between the
1663 reference group and one or more groups.
1665 .. mdp-value:: constraint
1667 Center of mass pulling using a constraint between the reference
1668 group and one or more groups. The setup is identical to the
1669 option umbrella, except for the fact that a rigid constraint is
1670 applied instead of a harmonic potential.
1672 .. mdp-value:: constant-force
1674 Center of mass pulling using a linear potential and therefore a
1675 constant force. For this option there is no reference position
1676 and therefore the parameters :mdp:`pull-coord1-init` and
1677 :mdp:`pull-coord1-rate` are not used.
1679 .. mdp-value:: flat-bottom
1681 At distances above :mdp:`pull-coord1-init` a harmonic potential
1682 is applied, otherwise no potential is applied.
1684 .. mdp-value:: flat-bottom-high
1686 At distances below :mdp:`pull-coord1-init` a harmonic potential
1687 is applied, otherwise no potential is applied.
1689 .. mdp-value:: external-potential
1691 An external potential that needs to be provided by another
1694 .. mdp:: pull-coord1-potential-provider
1696 The name of the external module that provides the potential for
1697 the case where :mdp:`pull-coord1-type` is external-potential.
1699 .. mdp:: pull-coord1-geometry
1701 .. mdp-value:: distance
1703 Pull along the vector connecting the two groups. Components can
1704 be selected with :mdp:`pull-coord1-dim`.
1706 .. mdp-value:: direction
1708 Pull in the direction of :mdp:`pull-coord1-vec`.
1710 .. mdp-value:: direction-periodic
1712 As :mdp-value:`pull-coord1-geometry=direction`, but allows the distance to be larger
1713 than half the box size. With this geometry the box should not be
1714 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1715 the pull force is not added to virial.
1717 .. mdp-value:: direction-relative
1719 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1720 that points from the COM of a third to the COM of a fourth pull
1721 group. This means that 4 groups need to be supplied in
1722 :mdp:`pull-coord1-groups`. Note that the pull force will give
1723 rise to a torque on the pull vector, which is turn leads to
1724 forces perpendicular to the pull vector on the two groups
1725 defining the vector. If you want a pull group to move between
1726 the two groups defining the vector, simply use the union of
1727 these two groups as the reference group.
1729 .. mdp-value:: cylinder
1731 Designed for pulling with respect to a layer where the reference
1732 COM is given by a local cylindrical part of the reference group.
1733 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1734 the first of the two groups in :mdp:`pull-coord1-groups` a
1735 cylinder is selected around the axis going through the COM of
1736 the second group with direction :mdp:`pull-coord1-vec` with
1737 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1738 continously to zero as the radial distance goes from 0 to
1739 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1740 dependence gives rise to radial forces on both pull groups.
1741 Note that the radius should be smaller than half the box size.
1742 For tilted cylinders they should be even smaller than half the
1743 box size since the distance of an atom in the reference group
1744 from the COM of the pull group has both a radial and an axial
1745 component. This geometry is not supported with constraint
1748 .. mdp-value:: angle
1750 Pull along an angle defined by four groups. The angle is
1751 defined as the angle between two vectors: the vector connecting
1752 the COM of the first group to the COM of the second group and
1753 the vector connecting the COM of the third group to the COM of
1756 .. mdp-value:: angle-axis
1758 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1759 Thus, only the two groups that define the first vector need to be given.
1761 .. mdp-value:: dihedral
1763 Pull along a dihedral angle defined by six groups. These pairwise
1764 define three vectors: the vector connecting the COM of group 1
1765 to the COM of group 2, the COM of group 3 to the COM of group 4,
1766 and the COM of group 5 to the COM group 6. The dihedral angle is
1767 then defined as the angle between two planes: the plane spanned by the
1768 the two first vectors and the plane spanned the two last vectors.
1771 .. mdp:: pull-coord1-groups
1773 The group indices on which this pull coordinate will operate.
1774 The number of group indices required is geometry dependent.
1775 The first index can be 0, in which case an
1776 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1777 absolute reference the system is no longer translation invariant
1778 and one should think about what to do with the center of mass
1781 .. mdp:: pull-coord1-dim
1784 Selects the dimensions that this pull coordinate acts on and that
1785 are printed to the output files when
1786 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1787 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1788 components set to Y contribute to the distance. Thus setting this
1789 to Y Y N results in a distance in the x/y plane. With other
1790 geometries all dimensions with non-zero entries in
1791 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1792 dimensions only affect the output.
1794 .. mdp:: pull-coord1-origin
1797 The pull reference position for use with an absolute reference.
1799 .. mdp:: pull-coord1-vec
1802 The pull direction. :ref:`gmx grompp` normalizes the vector.
1804 .. mdp:: pull-coord1-start
1808 do not modify :mdp:`pull-coord1-init`
1812 add the COM distance of the starting conformation to
1813 :mdp:`pull-coord1-init`
1815 .. mdp:: pull-coord1-init
1818 The reference distance or reference angle at t=0.
1820 .. mdp:: pull-coord1-rate
1822 (0) [nm/ps] or [deg/ps]
1823 The rate of change of the reference position or reference angle.
1825 .. mdp:: pull-coord1-k
1827 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1828 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1829 The force constant. For umbrella pulling this is the harmonic force
1830 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1831 for angles). For constant force pulling this is the
1832 force constant of the linear potential, and thus the negative (!)
1833 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1834 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1835 Note that for angles the force constant is expressed in terms of radians
1836 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1838 .. mdp:: pull-coord1-kB
1840 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1841 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1842 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1843 :mdp:`free-energy` is turned on. The force constant is then (1 -
1844 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1846 AWH adaptive biasing
1847 ^^^^^^^^^^^^^^^^^^^^
1857 Adaptively bias a reaction coordinate using the AWH method and estimate
1858 the corresponding PMF. The PMF and other AWH data are written to energy
1859 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1860 the ``gmx awh`` tool. The AWH coordinate can be
1861 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1862 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1863 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1866 .. mdp:: awh-potential
1868 .. mdp-value:: convolved
1870 The applied biasing potential is the convolution of the bias function and a
1871 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1872 in a smooth potential function and force. The resolution of the potential is set
1873 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1875 .. mdp-value:: umbrella
1877 The potential bias is applied by controlling the position of an harmonic potential
1878 using Monte-Carlo sampling. The force constant is set with
1879 :mdp:`awh1-dim1-force-constant`. The umbrella location
1880 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1881 There are no advantages to using an umbrella.
1882 This option is mainly for comparison and testing purposes.
1884 .. mdp:: awh-share-multisim
1888 AWH will not share biases across simulations started with
1889 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1893 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1894 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1895 with the biases with the same :mdp:`awh1-share-group` value.
1896 The simulations should have the same AWH settings for sharing to make sense.
1897 :ref:`gmx mdrun` will check whether the simulations are technically
1898 compatible for sharing, but the user should check that bias sharing
1899 physically makes sense.
1903 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1904 where -1 indicates to generate a seed. Only used with
1905 :mdp-value:`awh-potential=umbrella`.
1910 Number of steps between printing AWH data to the energy file, should be
1911 a multiple of :mdp:`nstenergy`.
1913 .. mdp:: awh-nstsample
1916 Number of steps between sampling of the coordinate value. This sampling
1917 is the basis for updating the bias and estimating the PMF and other AWH observables.
1919 .. mdp:: awh-nsamples-update
1922 The number of coordinate samples used for each AWH update.
1923 The update interval in steps is :mdp:`awh-nstsample` times this value.
1928 The number of biases, each acting on its own coordinate.
1929 The following options should be specified
1930 for each bias although below only the options for bias number 1 is shown. Options for
1931 other bias indices are obtained by replacing '1' by the bias index.
1933 .. mdp:: awh1-error-init
1935 (10.0) [kJ mol\ :sup:`-1`]
1936 Estimated initial average error of the PMF for this bias. This value together with the
1937 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1938 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1940 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1941 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1942 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1943 then :mdp:`awh1-error-init` should reflect that knowledge.
1945 .. mdp:: awh1-growth
1947 .. mdp-value:: exp-linear
1949 Each bias keeps a reference weight histogram for the coordinate samples.
1950 Its size sets the magnitude of the bias function and free energy estimate updates
1951 (few samples corresponds to large updates and vice versa).
1952 Thus, its growth rate sets the maximum convergence rate.
1953 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1954 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1955 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1956 high free energy barriers have not yet been flattened by the bias.
1958 .. mdp-value:: linear
1960 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1961 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
1962 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
1964 .. mdp:: awh1-equilibrate-histogram
1968 Do not equilibrate histogram.
1972 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
1973 histogram of sampled weights is following the target distribution closely enough (specifically,
1974 at least 80% of the target region needs to have a local relative error of less than 20%). This
1975 option would typically only be used when :mdp:`awh1-share-group` > 0
1976 and the initial configurations poorly represent the target
1979 .. mdp:: awh1-target
1981 .. mdp-value:: constant
1983 The bias is tuned towards a constant (uniform) coordinate distribution
1984 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
1986 .. mdp-value:: cutoff
1988 Similar to :mdp-value:`awh1-target=constant`, but the target
1989 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
1990 where F is the free energy relative to the estimated global minimum.
1991 This provides a smooth switch of a flat target distribution in
1992 regions with free energy lower than the cut-off to a Boltzmann
1993 distribution in regions with free energy higher than the cut-off.
1995 .. mdp-value:: boltzmann
1997 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
1998 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
1999 would give the same coordinate distribution as sampling with a simulation temperature
2002 .. mdp-value:: local-boltzmann
2004 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
2005 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
2006 change of the bias only depends on the local sampling. This local convergence property is
2007 only compatible with :mdp-value:`awh1-growth=linear`, since for
2008 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
2010 .. mdp:: awh1-target-beta-scaling
2013 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
2014 it is the unitless beta scaling factor taking values in (0,1).
2016 .. mdp:: awh1-target-cutoff
2018 (0) [kJ mol\ :sup:`-1`]
2019 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2021 .. mdp:: awh1-user-data
2025 Initialize the PMF and target distribution with default values.
2029 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2030 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2031 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2032 The file name can be changed with the ``-awh`` option.
2033 The first :mdp:`awh1-ndim` columns of
2034 each input file should contain the coordinate values, such that each row defines a point in
2035 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
2036 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2037 be in the same column as written by :ref:`gmx awh`.
2039 .. mdp:: awh1-share-group
2043 Do not share the bias.
2045 .. mdp-value:: positive
2047 Share the bias and PMF estimates within and/or between simulations.
2048 Within a simulation, the bias will be shared between biases that have the
2049 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2050 With :mdp-value:`awh-share-multisim=yes` and
2051 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2052 Sharing may increase convergence initially, although the starting configurations
2053 can be critical, especially when sharing between many biases.
2054 Currently, positive group values should start at 1 and increase
2055 by 1 for each subsequent bias that is shared.
2060 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2061 The following options should be specified for each such dimension. Below only
2062 the options for dimension number 1 is shown. Options for other dimension indices are
2063 obtained by replacing '1' by the dimension index.
2065 .. mdp:: awh1-dim1-coord-provider
2069 The module providing the reaction coordinate for this dimension.
2070 Currently AWH can only act on pull coordinates.
2072 .. mdp:: awh1-dim1-coord-index
2075 Index of the pull coordinate defining this coordinate dimension.
2077 .. mdp:: awh1-dim1-force-constant
2079 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2080 Force constant for the (convolved) umbrella potential(s) along this
2081 coordinate dimension.
2083 .. mdp:: awh1-dim1-start
2086 Start value of the sampling interval along this dimension. The range of allowed
2087 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2088 For periodic geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2089 is allowed. The interval will then wrap around from +period/2 to -period/2.
2091 .. mdp:: awh1-dim1-end
2094 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2096 .. mdp:: awh1-dim1-period
2099 The period of this reaction coordinate, use 0 when the coordinate is not periodic.
2101 .. mdp:: awh1-dim1-diffusion
2103 (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps]
2104 Estimated diffusion constant for this coordinate dimension determining the initial
2105 biasing rate. This needs only be a rough estimate and should not critically
2106 affect the results unless it is set to something very low, leading to slow convergence,
2107 or very high, forcing the system far from equilibrium. Not setting this value
2108 explicitly generates a warning.
2110 .. mdp:: awh1-dim1-cover-diameter
2113 Diameter that needs to be sampled by a single simulation around a coordinate value
2114 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2115 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2116 across each coordinate value.
2117 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2118 (:mdp:`awh1-share-group`>0).
2119 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2120 for many sharing simulations does not guarantee transitions across free energy barriers.
2121 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2122 has independently sampled the whole interval.
2127 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2128 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2129 that can be used to achieve such a rotation.
2135 No enforced rotation will be applied. All enforced rotation options will
2136 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2141 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2142 under the :mdp:`rot-group0` option.
2144 .. mdp:: rot-ngroups
2147 Number of rotation groups.
2151 Name of rotation group 0 in the index file.
2156 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2157 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2158 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2163 Use mass weighted rotation group positions.
2168 Rotation vector, will get normalized.
2173 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2177 (0) [degree ps\ :sup:`-1`]
2178 Reference rotation rate of group 0.
2182 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2183 Force constant for group 0.
2185 .. mdp:: rot-slab-dist0
2188 Slab distance, if a flexible axis rotation type was chosen.
2190 .. mdp:: rot-min-gauss0
2193 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2194 (for the flexible axis potentials).
2198 (0.0001) [nm\ :sup:`2`]
2199 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2201 .. mdp:: rot-fit-method0
2204 Fitting method when determining the actual angle of a rotation group
2205 (can be one of ``rmsd``, ``norm``, or ``potential``).
2207 .. mdp:: rot-potfit-nsteps0
2210 For fit type ``potential``, the number of angular positions around the reference angle for which the
2211 rotation potential is evaluated.
2213 .. mdp:: rot-potfit-step0
2216 For fit type ``potential``, the distance in degrees between two angular positions.
2218 .. mdp:: rot-nstrout
2221 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2222 and the rotation potential energy.
2224 .. mdp:: rot-nstsout
2227 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2237 ignore distance restraint information in topology file
2239 .. mdp-value:: simple
2241 simple (per-molecule) distance restraints.
2243 .. mdp-value:: ensemble
2245 distance restraints over an ensemble of molecules in one
2246 simulation box. Normally, one would perform ensemble averaging
2247 over multiple simulations, using ``mdrun
2248 -multidir``. The environment
2249 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2250 within each ensemble (usually equal to the number of directories
2251 supplied to ``mdrun -multidir``).
2253 .. mdp:: disre-weighting
2255 .. mdp-value:: equal
2257 divide the restraint force equally over all atom pairs in the
2260 .. mdp-value:: conservative
2262 the forces are the derivative of the restraint potential, this
2263 results in an weighting of the atom pairs to the reciprocal
2264 seventh power of the displacement. The forces are conservative
2265 when :mdp:`disre-tau` is zero.
2267 .. mdp:: disre-mixed
2271 the violation used in the calculation of the restraint force is
2272 the time-averaged violation
2276 the violation used in the calculation of the restraint force is
2277 the square root of the product of the time-averaged violation
2278 and the instantaneous violation
2282 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2283 force constant for distance restraints, which is multiplied by a
2284 (possibly) different factor for each restraint given in the `fac`
2285 column of the interaction in the topology file.
2290 time constant for distance restraints running average. A value of
2291 zero turns off time averaging.
2293 .. mdp:: nstdisreout
2296 period between steps when the running time-averaged and
2297 instantaneous distances of all atom pairs involved in restraints
2298 are written to the energy file (can make the energy file very
2305 ignore orientation restraint information in topology file
2309 use orientation restraints, ensemble averaging can be performed
2310 with ``mdrun -multidir``
2314 (0) [kJ mol\ :sup:`-1`]
2315 force constant for orientation restraints, which is multiplied by a
2316 (possibly) different weight factor for each restraint, can be set
2317 to zero to obtain the orientations from a free simulation
2322 time constant for orientation restraints running average. A value
2323 of zero turns off time averaging.
2325 .. mdp:: orire-fitgrp
2327 fit group for orientation restraining. This group of atoms is used
2328 to determine the rotation **R** of the system with respect to the
2329 reference orientation. The reference orientation is the starting
2330 conformation of the first subsystem. For a protein, backbone is a
2333 .. mdp:: nstorireout
2336 period between steps when the running time-averaged and
2337 instantaneous orientations for all restraints, and the molecular
2338 order tensor are written to the energy file (can make the energy
2342 Free energy calculations
2343 ^^^^^^^^^^^^^^^^^^^^^^^^
2345 .. mdp:: free-energy
2349 Only use topology A.
2353 Interpolate between topology A (lambda=0) to topology B
2354 (lambda=1) and write the derivative of the Hamiltonian with
2355 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2356 or the Hamiltonian differences with respect to other lambda
2357 values (as specified with foreign lambda) to the energy file
2358 and/or to ``dhdl.xvg``, where they can be processed by, for
2359 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2360 are interpolated linearly as described in the manual. When
2361 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2362 used for the LJ and Coulomb interactions.
2366 Turns on expanded ensemble simulation, where the alchemical state
2367 becomes a dynamic variable, allowing jumping between different
2368 Hamiltonians. See the expanded ensemble options for controlling how
2369 expanded ensemble simulations are performed. The different
2370 Hamiltonians used in expanded ensemble simulations are defined by
2371 the other free energy options.
2373 .. mdp:: init-lambda
2376 starting value for lambda (float). Generally, this should only be
2377 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2378 other cases, :mdp:`init-lambda-state` should be specified
2379 instead. Must be greater than or equal to 0.
2381 .. mdp:: delta-lambda
2384 increment per time step for lambda
2386 .. mdp:: init-lambda-state
2389 starting value for the lambda state (integer). Specifies which
2390 columm of the lambda vector (:mdp:`coul-lambdas`,
2391 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2392 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2393 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2394 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2395 the first column, and so on.
2397 .. mdp:: fep-lambdas
2400 Zero, one or more lambda values for which Delta H values will be
2401 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2402 steps. Values must be between 0 and 1. Free energy differences
2403 between different lambda values can then be determined with
2404 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2405 other -lambdas keywords because all components of the lambda vector
2406 that are not specified will use :mdp:`fep-lambdas` (including
2407 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2409 .. mdp:: coul-lambdas
2412 Zero, one or more lambda values for which Delta H values will be
2413 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2414 steps. Values must be between 0 and 1. Only the electrostatic
2415 interactions are controlled with this component of the lambda
2416 vector (and only if the lambda=0 and lambda=1 states have differing
2417 electrostatic interactions).
2419 .. mdp:: vdw-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 van der Waals
2425 interactions are controlled with this component of the lambda
2428 .. mdp:: bonded-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 bonded interactions
2434 are controlled with this component of the lambda vector.
2436 .. mdp:: restraint-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 restraint
2442 interactions: dihedral restraints, and the pull code restraints are
2443 controlled with this component of the lambda vector.
2445 .. mdp:: mass-lambdas
2448 Zero, one or more lambda values for which Delta H values will be
2449 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2450 steps. Values must be between 0 and 1. Only the particle masses are
2451 controlled with this component of the lambda vector.
2453 .. mdp:: temperature-lambdas
2456 Zero, one or more lambda values for which Delta H values will be
2457 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2458 steps. Values must be between 0 and 1. Only the temperatures
2459 controlled with this component of the lambda vector. Note that
2460 these lambdas should not be used for replica exchange, only for
2461 simulated tempering.
2463 .. mdp:: calc-lambda-neighbors
2466 Controls the number of lambda values for which Delta H values will
2467 be calculated and written out, if :mdp:`init-lambda-state` has
2468 been set. A positive value will limit the number of lambda points
2469 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2470 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2471 has a value of 2, energies for lambda points 3-7 will be calculated
2472 and writen out. A value of -1 means all lambda points will be
2473 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2474 1 is sufficient, while for MBAR -1 should be used.
2479 the soft-core alpha parameter, a value of 0 results in linear
2480 interpolation of the LJ and Coulomb interactions
2485 the power of the radial term in the soft-core equation. Possible
2486 values are 6 and 48. 6 is more standard, and is the default. When
2487 48 is used, then sc-alpha should generally be much lower (between
2493 Whether to apply the soft-core free energy interaction
2494 transformation to the Columbic interaction of a molecule. Default
2495 is no, as it is generally more efficient to turn off the Coulomic
2496 interactions linearly before turning off the van der Waals
2497 interactions. Note that it is only taken into account when lambda
2498 states are used, not with :mdp:`couple-lambda0` /
2499 :mdp:`couple-lambda1`, and you can still turn off soft-core
2500 interactions by setting :mdp:`sc-alpha` to 0.
2505 the power for lambda in the soft-core function, only the values 1
2511 the soft-core sigma for particles which have a C6 or C12 parameter
2512 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2514 .. mdp:: couple-moltype
2516 Here one can supply a molecule type (as defined in the topology)
2517 for calculating solvation or coupling free energies. There is a
2518 special option ``system`` that couples all molecule types in the
2519 system. This can be useful for equilibrating a system starting from
2520 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2521 on. The Van der Waals interactions and/or charges in this molecule
2522 type can be turned on or off between lambda=0 and lambda=1,
2523 depending on the settings of :mdp:`couple-lambda0` and
2524 :mdp:`couple-lambda1`. If you want to decouple one of several
2525 copies of a molecule, you need to copy and rename the molecule
2526 definition in the topology.
2528 .. mdp:: couple-lambda0
2530 .. mdp-value:: vdw-q
2532 all interactions are on at lambda=0
2536 the charges are zero (no Coulomb interactions) at lambda=0
2540 the Van der Waals interactions are turned at lambda=0; soft-core
2541 interactions will be required to avoid singularities
2545 the Van der Waals interactions are turned off and the charges
2546 are zero at lambda=0; soft-core interactions will be required to
2547 avoid singularities.
2549 .. mdp:: couple-lambda1
2551 analogous to :mdp:`couple-lambda1`, but for lambda=1
2553 .. mdp:: couple-intramol
2557 All intra-molecular non-bonded interactions for moleculetype
2558 :mdp:`couple-moltype` are replaced by exclusions and explicit
2559 pair interactions. In this manner the decoupled state of the
2560 molecule corresponds to the proper vacuum state without
2561 periodicity effects.
2565 The intra-molecular Van der Waals and Coulomb interactions are
2566 also turned on/off. This can be useful for partitioning
2567 free-energies of relatively large molecules, where the
2568 intra-molecular non-bonded interactions might lead to
2569 kinetically trapped vacuum conformations. The 1-4 pair
2570 interactions are not turned off.
2575 the frequency for writing dH/dlambda and possibly Delta H to
2576 dhdl.xvg, 0 means no ouput, should be a multiple of
2577 :mdp:`nstcalcenergy`.
2579 .. mdp:: dhdl-derivatives
2583 If yes (the default), the derivatives of the Hamiltonian with
2584 respect to lambda at each :mdp:`nstdhdl` step are written
2585 out. These values are needed for interpolation of linear energy
2586 differences with :ref:`gmx bar` (although the same can also be
2587 achieved with the right foreign lambda setting, that may not be as
2588 flexible), or with thermodynamic integration
2590 .. mdp:: dhdl-print-energy
2594 Include either the total or the potential energy in the dhdl
2595 file. Options are 'no', 'potential', or 'total'. This information
2596 is needed for later free energy analysis if the states of interest
2597 are at different temperatures. If all states are at the same
2598 temperature, this information is not needed. 'potential' is useful
2599 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2600 file. When rerunning from an existing trajectory, the kinetic
2601 energy will often not be correct, and thus one must compute the
2602 residual free energy from the potential alone, with the kinetic
2603 energy component computed analytically.
2605 .. mdp:: separate-dhdl-file
2609 The free energy values that are calculated (as specified with
2610 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2611 written out to a separate file, with the default name
2612 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2617 The free energy values are written out to the energy output file
2618 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2619 steps), where they can be extracted with :ref:`gmx energy` or
2620 used directly with :ref:`gmx bar`.
2622 .. mdp:: dh-hist-size
2625 If nonzero, specifies the size of the histogram into which the
2626 Delta H values (specified with foreign lambda) and the derivative
2627 dH/dl values are binned, and written to ener.edr. This can be used
2628 to save disk space while calculating free energy differences. One
2629 histogram gets written for each foreign lambda and two for the
2630 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2631 histogram settings (too small size or too wide bins) can introduce
2632 errors. Do not use histograms unless you're certain you need it.
2634 .. mdp:: dh-hist-spacing
2637 Specifies the bin width of the histograms, in energy units. Used in
2638 conjunction with :mdp:`dh-hist-size`. This size limits the
2639 accuracy with which free energies can be calculated. Do not use
2640 histograms unless you're certain you need it.
2643 Expanded Ensemble calculations
2644 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2646 .. mdp:: nstexpanded
2648 The number of integration steps beween attempted moves changing the
2649 system Hamiltonian in expanded ensemble simulations. Must be a
2650 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2657 No Monte Carlo in state space is performed.
2659 .. mdp-value:: metropolis-transition
2661 Uses the Metropolis weights to update the expanded ensemble
2662 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2665 .. mdp-value:: barker-transition
2667 Uses the Barker transition critera to update the expanded
2668 ensemble weight of each state i, defined by exp(-beta_new
2669 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2671 .. mdp-value:: wang-landau
2673 Uses the Wang-Landau algorithm (in state space, not energy
2674 space) to update the expanded ensemble weights.
2676 .. mdp-value:: min-variance
2678 Uses the minimum variance updating method of Escobedo et al. to
2679 update the expanded ensemble weights. Weights will not be the
2680 free energies, but will rather emphasize states that need more
2681 sampling to give even uncertainty.
2683 .. mdp:: lmc-mc-move
2687 No Monte Carlo in state space is performed.
2689 .. mdp-value:: metropolis-transition
2691 Randomly chooses a new state up or down, then uses the
2692 Metropolis critera to decide whether to accept or reject:
2693 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2695 .. mdp-value:: barker-transition
2697 Randomly chooses a new state up or down, then uses the Barker
2698 transition critera to decide whether to accept or reject:
2699 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2701 .. mdp-value:: gibbs
2703 Uses the conditional weights of the state given the coordinate
2704 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2707 .. mdp-value:: metropolized-gibbs
2709 Uses the conditional weights of the state given the coordinate
2710 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2711 to move to, EXCLUDING the current state, then uses a rejection
2712 step to ensure detailed balance. Always more efficient that
2713 Gibbs, though only marginally so in many situations, such as
2714 when only the nearest neighbors have decent phase space
2720 random seed to use for Monte Carlo moves in state space. When
2721 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2723 .. mdp:: mc-temperature
2725 Temperature used for acceptance/rejection for Monte Carlo moves. If
2726 not specified, the temperature of the simulation specified in the
2727 first group of :mdp:`ref-t` is used.
2732 The cutoff for the histogram of state occupancies to be reset, and
2733 the free energy incrementor to be changed from delta to delta *
2734 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2735 each histogram) / (average number of samples at each
2736 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2737 histogram is only considered flat if all Nratio > 0.8 AND
2738 simultaneously all 1/Nratio > 0.8.
2743 Each time the histogram is considered flat, then the current value
2744 of the Wang-Landau incrementor for the free energies is multiplied
2745 by :mdp:`wl-scale`. Value must be between 0 and 1.
2747 .. mdp:: init-wl-delta
2750 The initial value of the Wang-Landau incrementor in kT. Some value
2751 near 1 kT is usually most efficient, though sometimes a value of
2752 2-3 in units of kT works better if the free energy differences are
2755 .. mdp:: wl-oneovert
2758 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2759 the large sample limit. There is significant evidence that the
2760 standard Wang-Landau algorithms in state space presented here
2761 result in free energies getting 'burned in' to incorrect values
2762 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2763 then when the incrementor becomes less than 1/N, where N is the
2764 mumber of samples collected (and thus proportional to the data
2765 collection time, hence '1 over t'), then the Wang-Lambda
2766 incrementor is set to 1/N, decreasing every step. Once this occurs,
2767 :mdp:`wl-ratio` is ignored, but the weights will still stop
2768 updating when the equilibration criteria set in
2769 :mdp:`lmc-weights-equil` is achieved.
2771 .. mdp:: lmc-repeats
2774 Controls the number of times that each Monte Carlo swap type is
2775 performed each iteration. In the limit of large numbers of Monte
2776 Carlo repeats, then all methods converge to Gibbs sampling. The
2777 value will generally not need to be different from 1.
2779 .. mdp:: lmc-gibbsdelta
2782 Limit Gibbs sampling to selected numbers of neighboring states. For
2783 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2784 sampling over all of the states that are defined. A positive value
2785 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2786 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2787 value of -1 means that all states are considered. For less than 100
2788 states, it is probably not that expensive to include all states.
2790 .. mdp:: lmc-forced-nstart
2793 Force initial state space sampling to generate weights. In order to
2794 come up with reasonable initial weights, this setting allows the
2795 simulation to drive from the initial to the final lambda state,
2796 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2797 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2798 sufficiently long (thousands of steps, perhaps), then the weights
2799 will be close to correct. However, in most cases, it is probably
2800 better to simply run the standard weight equilibration algorithms.
2802 .. mdp:: nst-transition-matrix
2805 Frequency of outputting the expanded ensemble transition matrix. A
2806 negative number means it will only be printed at the end of the
2809 .. mdp:: symmetrized-transition-matrix
2812 Whether to symmetrize the empirical transition matrix. In the
2813 infinite limit the matrix will be symmetric, but will diverge with
2814 statistical noise for short timescales. Forced symmetrization, by
2815 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2816 like the existence of (small magnitude) negative eigenvalues.
2818 .. mdp:: mininum-var-min
2821 The min-variance strategy (option of :mdp:`lmc-stats` is only
2822 valid for larger number of samples, and can get stuck if too few
2823 samples are used at each state. :mdp:`mininum-var-min` is the
2824 minimum number of samples that each state that are allowed before
2825 the min-variance strategy is activated if selected.
2827 .. mdp:: init-lambda-weights
2829 The initial weights (free energies) used for the expanded ensemble
2830 states. Default is a vector of zero weights. format is similar to
2831 the lambda vector settings in :mdp:`fep-lambdas`, except the
2832 weights can be any floating point number. Units are kT. Its length
2833 must match the lambda vector lengths.
2835 .. mdp:: lmc-weights-equil
2839 Expanded ensemble weights continue to be updated throughout the
2844 The input expanded ensemble weights are treated as equilibrated,
2845 and are not updated throughout the simulation.
2847 .. mdp-value:: wl-delta
2849 Expanded ensemble weight updating is stopped when the
2850 Wang-Landau incrementor falls below this value.
2852 .. mdp-value:: number-all-lambda
2854 Expanded ensemble weight updating is stopped when the number of
2855 samples at all of the lambda states is greater than this value.
2857 .. mdp-value:: number-steps
2859 Expanded ensemble weight updating is stopped when the number of
2860 steps is greater than the level specified by this value.
2862 .. mdp-value:: number-samples
2864 Expanded ensemble weight updating is stopped when the number of
2865 total samples across all lambda states is greater than the level
2866 specified by this value.
2868 .. mdp-value:: count-ratio
2870 Expanded ensemble weight updating is stopped when the ratio of
2871 samples at the least sampled lambda state and most sampled
2872 lambda state greater than this value.
2874 .. mdp:: simulated-tempering
2877 Turn simulated tempering on or off. Simulated tempering is
2878 implemented as expanded ensemble sampling with different
2879 temperatures instead of different Hamiltonians.
2881 .. mdp:: sim-temp-low
2884 Low temperature for simulated tempering.
2886 .. mdp:: sim-temp-high
2889 High temperature for simulated tempering.
2891 .. mdp:: simulated-tempering-scaling
2893 Controls the way that the temperatures at intermediate lambdas are
2894 calculated from the :mdp:`temperature-lambdas` part of the lambda
2897 .. mdp-value:: linear
2899 Linearly interpolates the temperatures using the values of
2900 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2901 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2902 a temperature of 350. A nonlinear set of temperatures can always
2903 be implemented with uneven spacing in lambda.
2905 .. mdp-value:: geometric
2907 Interpolates temperatures geometrically between
2908 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2909 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2910 :mdp:`sim-temp-low`) raised to the power of
2911 (i/(ntemps-1)). This should give roughly equal exchange for
2912 constant heat capacity, though of course things simulations that
2913 involve protein folding have very high heat capacity peaks.
2915 .. mdp-value:: exponential
2917 Interpolates temperatures exponentially between
2918 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2919 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2920 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2921 (i))-1)/(exp(1.0)-i)).
2929 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2930 in groups Protein and Sol will experience constant acceleration as
2931 specified in the :mdp:`accelerate` line
2935 (0) [nm ps\ :sup:`-2`]
2936 acceleration for :mdp:`acc-grps`; x, y and z for each group
2937 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2938 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
2943 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2944 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2945 specifies for which dimension(s) the freezing applies. To avoid
2946 spurious contributions to the virial and pressure due to large
2947 forces between completely frozen atoms you need to use energy group
2948 exclusions, this also saves computing time. Note that coordinates
2949 of frozen atoms are not scaled by pressure-coupling algorithms.
2953 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2954 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
2955 N N N N`` means that particles in the first group can move only in
2956 Z direction. The particles in the second group can move in any
2959 .. mdp:: cos-acceleration
2961 (0) [nm ps\ :sup:`-2`]
2962 the amplitude of the acceleration profile for calculating the
2963 viscosity. The acceleration is in the X-direction and the magnitude
2964 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2965 added to the energy file: the amplitude of the velocity profile and
2970 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
2971 The velocities of deformation for the box elements: a(x) b(y) c(z)
2972 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2973 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2974 elements are corrected for periodicity. The coordinates are
2975 transformed accordingly. Frozen degrees of freedom are (purposely)
2976 also transformed. The time ts is set to t at the first step and at
2977 steps at which x and v are written to trajectory to ensure exact
2978 restarts. Deformation can be used together with semiisotropic or
2979 anisotropic pressure coupling when the appropriate
2980 compressibilities are set to zero. The diagonal elements can be
2981 used to strain a solid. The off-diagonal elements can be used to
2982 shear a solid or a liquid.
2988 .. mdp:: electric-field-x ; electric-field-y ; electric-field-z
2990 Here you can specify an electric field that optionally can be
2991 alternating and pulsed. The general expression for the field
2992 has the form of a gaussian laser pulse:
2994 E(t) = E0 exp ( -(t-t0)\ :sup:`2`/(2 sigma\ :sup:`2`) ) cos(omega (t-t0))
2996 For example, the four parameters for direction x are set in the
2997 three fields of :mdp:`electric-field-x` (and similar for y and z)
3000 electric-field-x = E0 omega t0 sigma
3002 In the special case that sigma = 0, the exponential term is omitted
3003 and only the cosine term is used. If also omega = 0 a static
3004 electric field is applied.
3006 More details in Carl Caleman and David van der Spoel: Picosecond
3007 Melting of Ice by an Infrared Laser Pulse - A Simulation Study.
3008 Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008)
3012 Mixed quantum/classical molecular dynamics
3013 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3023 Do a QM/MM simulation. Several groups can be described at
3024 different QM levels separately. These are specified in the
3025 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
3026 initio* theory at which the groups are described is specified by
3027 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
3028 groups at different levels of theory is only possible with the
3029 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
3033 groups to be descibed at the QM level
3037 .. mdp-value:: normal
3039 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
3040 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
3041 *ab initio* theory. The rest of the system is described at the
3042 MM level. The QM and MM subsystems interact as follows: MM point
3043 charges are included in the QM one-electron hamiltonian and all
3044 Lennard-Jones interactions are described at the MM level.
3046 .. mdp-value:: ONIOM
3048 The interaction between the subsystem is described using the
3049 ONIOM method by Morokuma and co-workers. There can be more than
3050 one :mdp:`QMMM-grps` each modeled at a different level of QM
3051 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
3056 Method used to compute the energy and gradients on the QM
3057 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
3058 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
3059 included in the active space is specified by :mdp:`CASelectrons`
3060 and :mdp:`CASorbitals`.
3065 Basis set used to expand the electronic wavefuntion. Only Gaussian
3066 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3067 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
3072 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
3073 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
3074 layer needs to be specified separately.
3079 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
3080 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
3081 needs to be specified separately.
3083 .. mdp:: CASorbitals
3086 The number of orbitals to be included in the active space when
3087 doing a CASSCF computation.
3089 .. mdp:: CASelectrons
3092 The number of electrons to be included in the active space when
3093 doing a CASSCF computation.
3099 No surface hopping. The system is always in the electronic
3104 Do a QM/MM MD simulation on the excited state-potential energy
3105 surface and enforce a *diabatic* hop to the ground-state when
3106 the system hits the conical intersection hyperline in the course
3107 the simulation. This option only works in combination with the
3111 Computational Electrophysiology
3112 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3113 Use these options to switch on and control ion/water position exchanges in "Computational
3114 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3120 Do not enable ion/water position exchanges.
3122 .. mdp-value:: X ; Y ; Z
3124 Allow for ion/water position exchanges along the chosen direction.
3125 In a typical setup with the membranes parallel to the x-y plane,
3126 ion/water pairs need to be exchanged in Z direction to sustain the
3127 requested ion concentrations in the compartments.
3129 .. mdp:: swap-frequency
3131 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3132 per compartment are determined and exchanges made if necessary.
3133 Normally it is not necessary to check at every time step.
3134 For typical Computational Electrophysiology setups, a value of about 100 is
3135 sufficient and yields a negligible performance impact.
3137 .. mdp:: split-group0
3139 Name of the index group of the membrane-embedded part of channel #0.
3140 The center of mass of these atoms defines one of the compartment boundaries
3141 and should be chosen such that it is near the center of the membrane.
3143 .. mdp:: split-group1
3145 Channel #1 defines the position of the other compartment boundary.
3147 .. mdp:: massw-split0
3149 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3153 Use the geometrical center.
3157 Use the center of mass.
3159 .. mdp:: massw-split1
3161 (no) As above, but for split-group #1.
3163 .. mdp:: solvent-group
3165 Name of the index group of solvent molecules.
3167 .. mdp:: coupl-steps
3169 (10) Average the number of ions per compartment over these many swap attempt steps.
3170 This can be used to prevent that ions near a compartment boundary
3171 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3175 (1) The number of different ion types to be controlled. These are during the
3176 simulation exchanged with solvent molecules to reach the desired reference numbers.
3178 .. mdp:: iontype0-name
3180 Name of the first ion type.
3182 .. mdp:: iontype0-in-A
3184 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3185 The default value of -1 means: use the number of ions as found in time step 0
3188 .. mdp:: iontype0-in-B
3190 (-1) Reference number of ions of type 0 for compartment B.
3192 .. mdp:: bulk-offsetA
3194 (0.0) Offset of the first swap layer from the compartment A midplane.
3195 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3196 at maximum distance (= bulk concentration) to the split group layers. However,
3197 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3198 towards one of the compartment-partitioning layers (at +/- 1.0).
3200 .. mdp:: bulk-offsetB
3202 (0.0) Offset of the other swap layer from the compartment B midplane.
3207 (\1) Only swap ions if threshold difference to requested count is reached.
3211 (2.0) [nm] Radius of the split cylinder #0.
3212 Two split cylinders (mimicking the channel pores) can optionally be defined
3213 relative to the center of the split group. With the help of these cylinders
3214 it can be counted which ions have passed which channel. The split cylinder
3215 definition has no impact on whether or not ion/water swaps are done.
3219 (1.0) [nm] Upper extension of the split cylinder #0.
3223 (1.0) [nm] Lower extension of the split cylinder #0.
3227 (2.0) [nm] Radius of the split cylinder #1.
3231 (1.0) [nm] Upper extension of the split cylinder #1.
3235 (1.0) [nm] Lower extension of the split cylinder #1.
3238 User defined thingies
3239 ^^^^^^^^^^^^^^^^^^^^^
3243 .. mdp:: userint1 (0)
3244 .. mdp:: userint2 (0)
3245 .. mdp:: userint3 (0)
3246 .. mdp:: userint4 (0)
3247 .. mdp:: userreal1 (0)
3248 .. mdp:: userreal2 (0)
3249 .. mdp:: userreal3 (0)
3250 .. mdp:: userreal4 (0)
3252 These you can use if you modify code. You can pass integers and
3253 reals and groups to your subroutine. Check the inputrec definition
3254 in ``src/gromacs/mdtypes/inputrec.h``
3259 These features have been removed from |Gromacs|, but so that old
3260 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3261 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3262 fatal error if this is set.
3268 .. mdp:: implicit-solvent
3272 .. _reference manual: gmx-manual-parent-dir_