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 ============================================
14 Default values are given in parentheses, or listed first among
15 choices. The first option in the list is always the default
16 option. Units are given in square brackets The difference between a
17 dash and an underscore is ignored.
19 A :ref:`sample mdp file <mdp>` is available. This should be
20 appropriate to start a normal simulation. Edit it to suit your
21 specific needs and desires.
29 directories to include in your topology. Format:
30 ``-I/home/john/mylib -I../otherlib``
34 defines to pass to the preprocessor, default is no defines. You can
35 use any defines to control options in your customized topology
36 files. Options that act on existing :ref:`top` file mechanisms
39 ``-DFLEXIBLE`` will use flexible water instead of rigid water
40 into your topology, this can be useful for normal mode analysis.
42 ``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
43 your topology, used for implementing position restraints.
51 (Despite the name, this list includes algorithms that are not
52 actually integrators over time. :mdp-value:`integrator=steep` and
53 all entries following it are in this category)
57 A leap-frog algorithm for integrating Newton's equations of motion.
61 A velocity Verlet algorithm for integrating Newton's equations
62 of motion. For constant NVE simulations started from
63 corresponding points in the same trajectory, the trajectories
64 are analytically, but not binary, identical to the
65 :mdp-value:`integrator=md` leap-frog integrator. The the kinetic
66 energy, which is determined from the whole step velocities and
67 is therefore slightly too high. The advantage of this integrator
68 is more accurate, reversible Nose-Hoover and Parrinello-Rahman
69 coupling integration based on Trotter expansion, as well as
70 (slightly too small) full step velocity output. This all comes
71 at the cost off extra computation, especially with constraints
72 and extra communication in parallel. Note that for nearly all
73 production simulations the :mdp-value:`integrator=md` integrator
76 .. mdp-value:: md-vv-avek
78 A velocity Verlet algorithm identical to
79 :mdp-value:`integrator=md-vv`, except that the kinetic energy is
80 determined as the average of the two half step kinetic energies
81 as in the :mdp-value:`integrator=md` integrator, and this thus
82 more accurate. With Nose-Hoover and/or Parrinello-Rahman
83 coupling this comes with a slight increase in computational
88 An accurate and efficient leap-frog stochastic dynamics
89 integrator. With constraints, coordinates needs to be
90 constrained twice per integration step. Depending on the
91 computational cost of the force calculation, this can take a
92 significant part of the simulation time. The temperature for one
93 or more groups of atoms (:mdp:`tc-grps`) is set with
94 :mdp:`ref-t`, the inverse friction constant for each group is
95 set with :mdp:`tau-t`. The parameter :mdp:`tcoupl` is
96 ignored. The random generator is initialized with
97 :mdp:`ld-seed`. When used as a thermostat, an appropriate value
98 for :mdp:`tau-t` is 2 ps, since this results in a friction that
99 is lower than the internal friction of water, while it is high
100 enough to remove excess heat NOTE: temperature deviations decay
101 twice as fast as with a Berendsen thermostat with the same
106 This used to be the default sd integrator, but is now
107 deprecated. Four Gaussian random numbers are required per
108 coordinate per step. With constraints, the temperature will be
113 An Euler integrator for Brownian or position Langevin dynamics,
114 the velocity is the force divided by a friction coefficient
115 (:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
116 :mdp:`bd-fric` is 0, the friction coefficient for each particle
117 is calculated as mass/ :mdp:`tau-t`, as for the integrator
118 :mdp-value:`integrator=sd`. The random generator is initialized
123 A steepest descent algorithm for energy minimization. The
124 maximum step size is :mdp:`emstep`, the tolerance is
129 A conjugate gradient algorithm for energy minimization, the
130 tolerance is :mdp:`emtol`. CG is more efficient when a steepest
131 descent step is done every once in a while, this is determined
132 by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
133 analysis, which requires a very high accuracy, |Gromacs| should be
134 compiled in double precision.
136 .. mdp-value:: l-bfgs
138 A quasi-Newtonian algorithm for energy minimization according to
139 the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
140 practice this seems to converge faster than Conjugate Gradients,
141 but due to the correction steps necessary it is not (yet)
146 Normal mode analysis is performed on the structure in the :ref:`tpr`
147 file. |Gromacs| should be compiled in double precision.
151 Test particle insertion. The last molecule in the topology is
152 the test particle. A trajectory must be provided to ``mdrun
153 -rerun``. This trajectory should not contain the molecule to be
154 inserted. Insertions are performed :mdp:`nsteps` times in each
155 frame at random locations and with random orientiations of the
156 molecule. When :mdp:`nstlist` is larger than one,
157 :mdp:`nstlist` insertions are performed in a sphere with radius
158 :mdp:`rtpi` around a the same random location using the same
159 neighborlist (and the same long-range energy when :mdp:`rvdw`
160 or :mdp:`rcoulomb` > :mdp:`rlist`, which is only allowed for
161 single-atom molecules). Since neighborlist construction is
162 expensive, one can perform several extra insertions with the
163 same list almost for free. The random seed is set with
164 :mdp:`ld-seed`. The temperature for the Boltzmann weighting is
165 set with :mdp:`ref-t`, this should match the temperature of the
166 simulation of the original trajectory. Dispersion correction is
167 implemented correctly for TPI. All relevant quantities are
168 written to the file specified with ``mdrun -tpi``. The
169 distribution of insertion energies is written to the file
170 specified with ``mdrun -tpid``. No trajectory or energy file is
171 written. Parallel TPI gives identical results to single-node
172 TPI. For charged molecules, using PME with a fine grid is most
173 accurate and also efficient, since the potential in the system
174 only needs to be calculated once per frame.
178 Test particle insertion into a predefined cavity location. The
179 procedure is the same as for :mdp-value:`integrator=tpi`, except
180 that one coordinate extra is read from the trajectory, which is
181 used as the insertion location. The molecule to be inserted
182 should be centered at 0,0,0. |Gromacs| does not do this for you,
183 since for different situations a different way of centering
184 might be optimal. Also :mdp:`rtpi` sets the radius for the
185 sphere around this location. Neighbor searching is done only
186 once per frame, :mdp:`nstlist` is not used. Parallel
187 :mdp-value:`integrator=tpic` gives identical results to
188 single-rank :mdp-value:`integrator=tpic`.
193 starting time for your run (only makes sense for time-based
199 time step for integration (only makes sense for time-based
205 maximum number of steps to integrate or minimize, -1 is no
211 The starting step. The time at an step i in a run is
212 calculated as: t = :mdp:`tinit` + :mdp:`dt` *
213 (:mdp:`init-step` + i). The free-energy lambda is calculated
214 as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
215 (:mdp:`init-step` + i). Also non-equilibrium MD parameters can
216 depend on the step number. Thus for exact restarts or redoing
217 part of a run it might be necessary to set :mdp:`init-step` to
218 the step number of the restart frame. :ref:`gmx convert-tpr`
219 does this automatically.
223 .. mdp-value:: Linear
225 Remove center of mass translation
227 .. mdp-value:: Angular
229 Remove center of mass translation and rotation around the center of mass
233 No restriction on the center of mass motion
238 frequency for center of mass motion removal
242 group(s) for center of mass motion removal, default is the whole
252 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
253 the friction coefficient for each particle is calculated as mass/
259 used to initialize random generator for thermal noise for
260 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
261 a pseudo random seed is used. When running BD or SD on multiple
262 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
263 the processor number.
271 (10.0) \[kJ mol-1 nm-1\]
272 the minimization is converged when the maximum force is smaller
283 frequency of performing 1 steepest descent step while doing
284 conjugate gradient energy minimization.
289 Number of correction steps to use for L-BFGS minimization. A higher
290 number is (at least theoretically) more accurate, but slower.
293 Shell Molecular Dynamics
294 ^^^^^^^^^^^^^^^^^^^^^^^^
296 When shells or flexible constraints are present in the system the
297 positions of the shells and the lengths of the flexible constraints
298 are optimized at every time step until either the RMS force on the
299 shells and constraints is less than :mdp:`emtol`, or a maximum number
300 of iterations :mdp:`niter` has been reached. Minimization is converged
301 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
302 value should be 1.0 at most.
307 maximum number of iterations for optimizing the shell positions and
308 the flexible constraints.
313 the step size for optimizing the flexible constraints. Should be
314 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
315 particles in a flexible constraint and d2V/dq2 is the second
316 derivative of the potential in the constraint direction. Hopefully
317 this number does not differ too much between the flexible
318 constraints, as the number of iterations and thus the runtime is
319 very sensitive to fcstep. Try several values!
322 Test particle insertion
323 ^^^^^^^^^^^^^^^^^^^^^^^
328 the test particle insertion radius, see integrators
329 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
338 number of steps that elapse between writing coordinates to output
339 trajectory file, the last coordinates are always written
344 number of steps that elapse between writing velocities to output
345 trajectory, the last velocities are always written
350 number of steps that elapse between writing forces to output
356 number of steps that elapse between writing energies to the log
357 file, the last energies are always written
359 .. mdp:: nstcalcenergy
362 number of steps that elapse between calculating the energies, 0 is
363 never. This option is only relevant with dynamics. With a
364 twin-range cut-off setup :mdp:`nstcalcenergy` should be equal to
365 or a multiple of :mdp:`nstlist`. This option affects the
366 performance in parallel simulations, because calculating energies
367 requires global communication between all processes which can
368 become a bottleneck at high parallelization.
373 number of steps that else between writing energies to energy file,
374 the last energies are always written, should be a multiple of
375 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
376 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
377 energy file, so :ref:`gmx energy` can report exact energy averages
378 and fluctuations also when :mdp:`nstenergy` > 1
380 .. mdp:: nstxout-compressed
383 number of steps that elapse between writing position coordinates
384 using lossy compression
386 .. mdp:: compressed-x-precision
389 precision with which to write to the compressed trajectory file
391 .. mdp:: compressed-x-grps
393 group(s) to write to the compressed trajectory file, by default the
394 whole system is written (if :mdp:`nstxout-compressed` > 0)
398 group(s) for which to write to write short-ranged non-bonded
399 potential energies to the energy file (not supported on GPUs)
405 .. mdp:: cutoff-scheme
407 .. mdp-value:: Verlet
409 Generate a pair list with buffering. The buffer size is
410 automatically set based on :mdp:`verlet-buffer-tolerance`,
411 unless this is set to -1, in which case :mdp:`rlist` will be
412 used. This option has an explicit, exact cut-off at :mdp:`rvdw`
413 equal to :mdp:`rcoulomb`. Currently only cut-off,
414 reaction-field, PME electrostatics and plain LJ are
415 supported. Some :ref:`gmx mdrun` functionality is not yet
416 supported with the :mdp:`Verlet` scheme, but :ref:`gmx grompp`
417 checks for this. Native GPU acceleration is only supported with
418 :mdp:`Verlet`. With GPU-accelerated PME or with separate PME
419 ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
420 balance by scaling :mdp:`rcoulomb` and the grid spacing. This
421 can be turned off with ``mdrun -notunepme``. :mdp:`Verlet` is
422 faster than :mdp:`group` when there is no water, or if
423 :mdp:`group` would use a pair-list buffer to conserve energy.
427 Generate a pair list for groups of atoms. These groups
428 correspond to the charge groups in the topology. This was the
429 only cut-off treatment scheme before version 4.6, and is
430 **deprecated in |gmx-version|**. There is no explicit buffering of
431 the pair list. This enables efficient force calculations for
432 water, but energy is only conserved when a buffer is explicitly
441 Frequency to update the neighbor list (and the long-range
442 forces, when using twin-range cut-offs). When this is 0, the
443 neighbor list is made only once. With energy minimization the
444 neighborlist will be updated for every energy evaluation when
445 :mdp:`nstlist` is greater than 0. With :mdp:`Verlet` and
446 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
447 a minimum value and :ref:`gmx mdrun` might increase it, unless
448 it is set to 1. With parallel simulations and/or non-bonded
449 force calculation on the GPU, a value of 20 or 40 often gives
450 the best performance. With :mdp:`group` and non-exact
451 cut-off's, :mdp:`nstlist` will affect the accuracy of your
452 simulation and it can not be chosen freely.
456 The neighbor list is only constructed once and never
457 updated. This is mainly useful for vacuum simulations in which
458 all particles see each other.
467 Controls the period between calculations of long-range forces when
468 using the group cut-off scheme.
472 Calculate the long-range forces every single step. This is
473 useful to have separate neighbor lists with buffers for
474 electrostatics and Van der Waals interactions, and in particular
475 it makes it possible to have the Van der Waals cutoff longer
476 than electrostatics (useful *e.g.* with PME). However, there is
477 no point in having identical long-range cutoffs for both
478 interaction forms and update them every step - then it will be
479 slightly faster to put everything in the short-range list.
483 Calculate the long-range forces every :mdp:`nstcalclr` steps
484 and use a multiple-time-step integrator to combine forces. This
485 can now be done more frequently than :mdp:`nstlist` since the
486 lists are stored, and it might be a good idea *e.g.* for Van der
487 Waals interactions that vary slower than electrostatics.
491 Calculate long-range forces on steps where neighbor searching is
492 performed. While this is the default value, you might want to
493 consider updating the long-range forces more frequently.
495 Note that twin-range force evaluation might be enabled
496 automatically by PP-PME load balancing. This is done in order to
497 maintain the chosen Van der Waals interaction radius even if the
498 load balancing is changing the electrostatics cutoff. If the
499 :ref:`mdp` file already specifies twin-range interactions (*e.g.* to
500 evaluate Lennard-Jones interactions with a longer cutoff than
501 the PME electrostatics every 2-3 steps), the load balancing will
502 have also a small effect on Lennard-Jones, since the short-range
503 cutoff (inside which forces are evaluated every step) is
510 Make a grid in the box and only check atoms in neighboring grid
511 cells when constructing a new neighbor list every
512 :mdp:`nstlist` steps. In large systems grid search is much
513 faster than simple search.
515 .. mdp-value:: simple
517 Check every atom in the box when constructing a new neighbor
518 list every :mdp:`nstlist` steps (only with :mdp:`group`
525 Use periodic boundary conditions in all directions.
529 Use no periodic boundary conditions, ignore the box. To simulate
530 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
531 best performance without cut-offs on a single MPI rank, set
532 :mdp:`nstlist` to zero and :mdp:`ns-type` =simple.
536 Use periodic boundary conditions in x and y directions
537 only. This works only with :mdp:`ns-type` =grid and can be used
538 in combination with walls_. Without walls or with only one wall
539 the system size is infinite in the z direction. Therefore
540 pressure coupling or Ewald summation methods can not be
541 used. These disadvantages do not apply when two walls are used.
543 .. mdp:: periodic-molecules
547 molecules are finite, fast molecular PBC can be used
551 for systems with molecules that couple to themselves through the
552 periodic boundary conditions, this requires a slower PBC
553 algorithm and molecules are not made whole in the output
555 .. mdp:: verlet-buffer-tolerance
557 (0.005) \[kJ/mol/ps\]
559 Useful only with the :mdp:`Verlet` :mdp:`cutoff-scheme`. This sets
560 the maximum allowed error for pair interactions per particle caused
561 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
562 :mdp:`nstlist` and the Verlet buffer size are fixed (for
563 performance reasons), particle pairs not in the pair list can
564 occasionally get within the cut-off distance during
565 :mdp:`nstlist` -1 steps. This causes very small jumps in the
566 energy. In a constant-temperature ensemble, these very small energy
567 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
568 estimate assumes a homogeneous particle distribution, hence the
569 errors might be slightly underestimated for multi-phase
570 systems. (See the `reference manual`_ for details). For longer
571 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
572 overestimated, because the interactions between particles are
573 ignored. Combined with cancellation of errors, the actual drift of
574 the total energy is usually one to two orders of magnitude
575 smaller. Note that the generated buffer size takes into account
576 that the |Gromacs| pair-list setup leads to a reduction in the
577 drift by a factor 10, compared to a simple particle-pair based
578 list. Without dynamics (energy minimization etc.), the buffer is 5%
579 of the cut-off. For NVE simulations the initial temperature is
580 used, unless this is zero, in which case a buffer of 10% is
581 used. For NVE simulations the tolerance usually needs to be lowered
582 to achieve proper energy conservation on the nanosecond time
583 scale. To override the automated buffer setting, use
584 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
589 Cut-off distance for the short-range neighbor list. With the
590 :mdp:`Verlet` :mdp:`cutoff-scheme`, this is by default set by the
591 :mdp:`verlet-buffer-tolerance` option and the value of
592 :mdp:`rlist` is ignored.
597 Cut-off distance for the long-range neighbor list. This parameter
598 is only relevant for a twin-range cut-off setup with switched
599 potentials. In that case a buffer region is required to account for
600 the size of charge groups. In all other cases this parameter is
601 automatically set to the longest cut-off distance.
609 .. mdp-value:: Cut-off
611 Twin range cut-offs with neighborlist cut-off :mdp:`rlist` and
612 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rcoulomb` >=
617 Classical Ewald sum electrostatics. The real-space cut-off
618 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
619 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
620 of wave vectors used in reciprocal space is controlled by
621 :mdp:`fourierspacing`. The relative accuracy of
622 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
624 NOTE: Ewald scales as O(N^3/2) and is thus extremely slow for
625 large systems. It is included mainly for reference - in most
626 cases PME will perform much better.
630 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
631 space is similar to the Ewald sum, while the reciprocal part is
632 performed with FFTs. Grid dimensions are controlled with
633 :mdp:`fourierspacing` and the interpolation order with
634 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
635 interpolation the electrostatic forces have an accuracy of
636 2-3*10^-4. Since the error from the vdw-cutoff is larger than
637 this you might try 0.15 nm. When running in parallel the
638 interpolation parallelizes better than the FFT, so try
639 decreasing grid dimensions while increasing interpolation.
641 .. mdp-value:: P3M-AD
643 Particle-Particle Particle-Mesh algorithm with analytical
644 derivative for for long range electrostatic interactions. The
645 method and code is identical to SPME, except that the influence
646 function is optimized for the grid. This gives a slight increase
649 .. mdp-value:: Reaction-Field
651 Reaction field electrostatics with Coulomb cut-off
652 :mdp:`rcoulomb`, where :mdp:`rcoulomb` >= :mdp:`rlist`. The
653 dielectric constant beyond the cut-off is
654 :mdp:`epsilon-rf`. The dielectric constant can be set to
655 infinity by setting :mdp:`epsilon-rf` =0.
657 .. mdp-value:: Generalized-Reaction-Field
659 Generalized reaction field with Coulomb cut-off
660 :mdp:`rcoulomb`, where :mdp:`rcoulomb` >= :mdp:`rlist`. The
661 dielectric constant beyond the cut-off is
662 :mdp:`epsilon-rf`. The ionic strength is computed from the
663 number of charged (*i.e.* with non zero charge) charge
664 groups. The temperature for the GRF potential is set with
667 .. mdp-value:: Reaction-Field-zero
669 In |Gromacs|, normal reaction-field electrostatics with
670 :mdp:`cutoff-scheme` = :mdp:`group` leads to bad energy
671 conservation. :mdp:`Reaction-Field-zero` solves this by making
672 the potential zero beyond the cut-off. It can only be used with
673 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
674 only for that value the force vanishes at the
675 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
676 :mdp:`rcoulomb` to accommodate for the size of charge groups
677 and diffusion between neighbor list updates. This, and the fact
678 that table lookups are used instead of analytical functions make
679 :mdp:`Reaction-Field-zero` computationally more expensive than
680 normal reaction-field.
682 .. mdp-value:: Reaction-Field-nec
684 The same as :mdp-value:`coulombtype=Reaction-Field`, but
685 implemented as in |Gromacs| versions before 3.3. No
686 reaction-field correction is applied to excluded atom pairs and
687 self pairs. The 1-4 interactions are calculated using a
688 reaction-field. The missing correction due to the excluded pairs
689 that do not have a 1-4 interaction is up to a few percent of the
690 total electrostatic energy and causes a minor difference in the
691 forces and the pressure.
695 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
696 might want to use :mdp:`Reaction-Field-zero` instead, which has
697 a similar potential shape, but has a physical interpretation and
698 has better energies due to the exclusion correction terms.
700 .. mdp-value:: Encad-Shift
702 The Coulomb potential is decreased over the whole range, using
703 the definition from the Encad simulation package.
705 .. mdp-value:: Switch
707 Analogous to :mdp-value:`vdwtype=Switch` for
708 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
709 serious artifacts, advice: use :mdp:`Reaction-Field-zero`
714 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
715 with user-defined potential functions for repulsion, dispersion
716 and Coulomb. When pair interactions are present, :ref:`gmx
717 mdrun` also expects to find a file ``tablep.xvg`` for the pair
718 interactions. When the same interactions should be used for
719 non-bonded and pair interactions the user can specify the same
720 file name for both table files. These files should contain 7
721 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
722 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
723 function, ``g(x)`` the dispersion function and ``h(x)`` the
724 repulsion function. When :mdp:`vdwtype` is not set to User the
725 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
726 the non-bonded interactions ``x`` values should run from 0 to
727 the largest cut-off distance + :mdp:`table-extension` and
728 should be uniformly spaced. For the pair interactions the table
729 length in the file will be used. The optimal spacing, which is
730 used for non-user tables, is ``0.002 nm`` when you run in mixed
731 precision or ``0.0005 nm`` when you run in double precision. The
732 function value at ``x=0`` is not important. More information is
733 in the printed manual.
735 .. mdp-value:: PME-Switch
737 A combination of PME and a switch function for the direct-space
738 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
739 :mdp:`rlist`. This is mainly useful constant energy simulations
740 (note that using PME with :mdp:`cutoff-scheme` = :mdp:`Verlet`
741 will be more efficient).
743 .. mdp-value:: PME-User
745 A combination of PME and user tables (see
746 above). :mdp:`rcoulomb` is allowed to be smaller than
747 :mdp:`rlist`. The PME mesh contribution is subtracted from the
748 user table by :ref:`gmx mdrun`. Because of this subtraction the
749 user tables should contain about 10 decimal places.
751 .. mdp-value:: PME-User-Switch
753 A combination of PME-User and a switching function (see
754 above). The switching function is applied to final
755 particle-particle interaction, *i.e.* both to the user supplied
756 function and the PME Mesh correction part.
758 .. mdp:: coulomb-modifier
760 .. mdp-value:: Potential-shift-Verlet
762 Selects Potential-shift with the Verlet cutoff-scheme, as it is
763 (nearly) free; selects None with the group cutoff-scheme.
765 .. mdp-value:: Potential-shift
767 Shift the Coulomb potential by a constant such that it is zero
768 at the cut-off. This makes the potential the integral of the
769 force. Note that this does not affect the forces or the
774 Use an unmodified Coulomb potential. With the group scheme this
775 means no exact cut-off is used, energies and forces are
776 calculated for all pairs in the neighborlist.
778 .. mdp:: rcoulomb-switch
781 where to start switching the Coulomb potential, only relevant
782 when force or potential switching is used
787 distance for the Coulomb cut-off
792 The relative dielectric constant. A value of 0 means infinity.
797 The relative dielectric constant of the reaction field. This
798 is only used with reaction-field electrostatics. A value of 0
807 .. mdp-value:: Cut-off
809 Twin range cut-offs with neighbor list cut-off :mdp:`rlist` and
810 VdW cut-off :mdp:`rvdw`, where :mdp:`rvdw` >= :mdp:`rlist`.
814 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
815 grid dimensions are controlled with :mdp:`fourierspacing` in
816 the same way as for electrostatics, and the interpolation order
817 is controlled with :mdp:`pme-order`. The relative accuracy of
818 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
819 and the specific combination rules that are to be used by the
820 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
824 This functionality is deprecated and replaced by
825 :mdp:`vdw-modifier` = Force-switch. The LJ (not Buckingham)
826 potential is decreased over the whole range and the forces decay
827 smoothly to zero between :mdp:`rvdw-switch` and
828 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
829 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
830 size of charge groups and diffusion between neighbor list
833 .. mdp-value:: Switch
835 This functionality is deprecated and replaced by
836 :mdp:`vdw-modifier` = Potential-switch. The LJ (not Buckingham)
837 potential is normal out to :mdp:`rvdw-switch`, after which it
838 is switched off to reach zero at :mdp:`rvdw`. Both the
839 potential and force functions are continuously smooth, but be
840 aware that all switch functions will give rise to a bulge
841 (increase) in the force (since we are switching the
842 potential). The neighbor search cut-off :mdp:`rlist` should be
843 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
844 size of charge groups and diffusion between neighbor list
847 .. mdp-value:: Encad-Shift
849 The LJ (not Buckingham) potential is decreased over the whole
850 range, using the definition from the Encad simulation package.
854 See user for :mdp:`coulombtype`. The function value at zero is
855 not important. When you want to use LJ correction, make sure
856 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
857 function. When :mdp:`coulombtype` is not set to User the values
858 for the ``f`` and ``-f'`` columns are ignored.
860 .. mdp:: vdw-modifier
862 .. mdp-value:: Potential-shift-Verlet
864 Selects Potential-shift with the Verlet cutoff-scheme, as it is
865 (nearly) free; selects None with the group cutoff-scheme.
867 .. mdp-value:: Potential-shift
869 Shift the Van der Waals potential by a constant such that it is
870 zero at the cut-off. This makes the potential the integral of
871 the force. Note that this does not affect the forces or the
876 Use an unmodified Van der Waals potential. With the group scheme
877 this means no exact cut-off is used, energies and forces are
878 calculated for all pairs in the neighborlist.
880 .. mdp-value:: Force-switch
882 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
883 and :mdp:`rvdw`. This shifts the potential shift over the whole
884 range and switches it to zero at the cut-off. Note that this is
885 more expensive to calculate than a plain cut-off and it is not
886 required for energy conservation, since Potential-shift
887 conserves energy just as well.
889 .. mdp-value:: Potential-switch
891 Smoothly switches the potential to zero between
892 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
893 articifically large forces in the switching region and is much
894 more expensive to calculate. This option should only be used if
895 the force field you are using requires this.
901 where to start switching the LJ force and possibly the potential,
902 only relevant when force or potential switching is used
907 distance for the LJ or Buckingham cut-off
913 don't apply any correction
915 .. mdp-value:: EnerPres
917 apply long range dispersion corrections for Energy and Pressure
921 apply long range dispersion corrections for Energy only
927 .. mdp:: table-extension
930 Extension of the non-bonded potential lookup tables beyond the
931 largest cut-off distance. The value should be large enough to
932 account for charge group sizes and the diffusion between
933 neighbor-list updates. Without user defined potential the same
934 table length is used for the lookup tables for the 1-4
935 interactions, which are always tabulated irrespective of the use of
936 tables for the non-bonded interactions. The value of
937 :mdp:`table-extension` in no way affects the values of
938 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
940 .. mdp:: energygrp-table
942 When user tables are used for electrostatics and/or VdW, here one
943 can give pairs of energy groups for which seperate user tables
944 should be used. The two energy groups will be appended to the table
945 file name, in order of their definition in :mdp:`energygrps`,
946 seperated by underscores. For example, if ``energygrps = Na Cl
947 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
948 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
949 normal ``table.xvg`` which will be used for all other energy group
956 .. mdp:: fourierspacing
959 For ordinary Ewald, the ratio of the box dimensions and the spacing
960 determines a lower bound for the number of wave vectors to use in
961 each (signed) direction. For PME and P3M, that ratio determines a
962 lower bound for the number of Fourier-space grid points that will
963 be used along that axis. In all cases, the number for each
964 direction can be overridden by entering a non-zero value for that
965 :mdp:`fourier-nx` direction. For optimizing the relative load of
966 the particle-particle interactions and the mesh part of PME, it is
967 useful to know that the accuracy of the electrostatics remains
968 nearly constant when the Coulomb cut-off and the PME grid spacing
969 are scaled by the same factor.
976 Highest magnitude of wave vectors in reciprocal space when using Ewald.
977 Grid size when using PME or P3M. These values override
978 :mdp:`fourierspacing` per direction. The best choice is powers of
979 2, 3, 5 and 7. Avoid large primes.
984 Interpolation order for PME. 4 equals cubic interpolation. You
985 might try 6/8/10 when running in parallel and simultaneously
986 decrease grid dimension.
991 The relative strength of the Ewald-shifted direct potential at
992 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
993 will give a more accurate direct sum, but then you need more wave
994 vectors for the reciprocal sum.
996 .. mdp:: ewald-rtol-lj
999 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
1000 to control the relative strength of the dispersion potential at
1001 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
1002 electrostatic potential.
1004 .. mdp:: lj-pme-comb-rule
1007 The combination rules used to combine VdW-parameters in the
1008 reciprocal part of LJ-PME. Geometric rules are much faster than
1009 Lorentz-Berthelot and usually the recommended choice, even when the
1010 rest of the force field uses the Lorentz-Berthelot rules.
1012 .. mdp-value:: Geometric
1014 Apply geometric combination rules
1016 .. mdp-value:: Lorentz-Berthelot
1018 Apply Lorentz-Berthelot combination rules
1020 .. mdp:: ewald-geometry
1024 The Ewald sum is performed in all three dimensions.
1028 The reciprocal sum is still performed in 3D, but a force and
1029 potential correction applied in the `z` dimension to produce a
1030 pseudo-2D summation. If your system has a slab geometry in the
1031 `x-y` plane you can try to increase the `z`-dimension of the box
1032 (a box height of 3 times the slab height is usually ok) and use
1035 .. mdp:: epsilon-surface
1038 This controls the dipole correction to the Ewald summation in
1039 3D. The default value of zero means it is turned off. Turn it on by
1040 setting it to the value of the relative permittivity of the
1041 imaginary surface around your infinite system. Be careful - you
1042 shouldn't use this if you have free mobile charges in your
1043 system. This value does not affect the slab 3DC variant of the long
1047 Temperature coupling
1048 ^^^^^^^^^^^^^^^^^^^^
1054 No temperature coupling.
1056 .. mdp-value:: berendsen
1058 Temperature coupling with a Berendsen-thermostat to a bath with
1059 temperature :mdp:`ref-t`, with time constant
1060 :mdp:`tau-t`. Several groups can be coupled separately, these
1061 are specified in the :mdp:`tc-grps` field separated by spaces.
1063 .. mdp-value:: nose-hoover
1065 Temperature coupling using a Nose-Hoover extended ensemble. The
1066 reference temperature and coupling groups are selected as above,
1067 but in this case :mdp:`tau-t` controls the period of the
1068 temperature fluctuations at equilibrium, which is slightly
1069 different from a relaxation time. For NVT simulations the
1070 conserved energy quantity is written to energy and log file.
1072 .. mdp-value:: andersen
1074 Temperature coupling by randomizing a fraction of the particles
1075 at each timestep. Reference temperature and coupling groups are
1076 selected as above. :mdp:`tau-t` is the average time between
1077 randomization of each molecule. Inhibits particle dynamics
1078 somewhat, but little or no ergodicity issues. Currently only
1079 implemented with velocity Verlet, and not implemented with
1082 .. mdp-value:: andersen-massive
1084 Temperature coupling by randomizing all particles at infrequent
1085 timesteps. Reference temperature and coupling groups are
1086 selected as above. :mdp:`tau-t` is the time between
1087 randomization of all molecules. Inhibits particle dynamics
1088 somewhat, but little or no ergodicity issues. Currently only
1089 implemented with velocity Verlet.
1091 .. mdp-value:: v-rescale
1093 Temperature coupling using velocity rescaling with a stochastic
1094 term (JCP 126, 014101). This thermostat is similar to Berendsen
1095 coupling, with the same scaling using :mdp:`tau-t`, but the
1096 stochastic term ensures that a proper canonical ensemble is
1097 generated. The random seed is set with :mdp:`ld-seed`. This
1098 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1099 simulations the conserved energy quantity is written to the
1100 energy and log file.
1105 The frequency for coupling the temperature. The default value of -1
1106 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1107 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1108 Verlet integrators :mdp:`nsttcouple` is set to 1.
1110 .. mdp:: nh-chain-length
1113 The number of chained Nose-Hoover thermostats for velocity Verlet
1114 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1115 only supports 1. Data for the NH chain variables is not printed to
1116 the :ref:`edr` file, but can be using the ``GMX_NOSEHOOVER_CHAINS``
1117 environment variable
1121 groups to couple to separate temperature baths
1126 time constant for coupling (one for each group in
1127 :mdp:`tc-grps`), -1 means no temperature coupling
1132 reference temperature for coupling (one for each group in
1143 No pressure coupling. This means a fixed box size.
1145 .. mdp-value:: Berendsen
1147 Exponential relaxation pressure coupling with time constant
1148 :mdp:`tau-p`. The box is scaled every timestep. It has been
1149 argued that this does not yield a correct thermodynamic
1150 ensemble, but it is the most efficient way to scale a box at the
1153 .. mdp-value:: Parrinello-Rahman
1155 Extended-ensemble pressure coupling where the box vectors are
1156 subject to an equation of motion. The equation of motion for the
1157 atoms is coupled to this. No instantaneous scaling takes
1158 place. As for Nose-Hoover temperature coupling the time constant
1159 :mdp:`tau-p` is the period of pressure fluctuations at
1160 equilibrium. This is probably a better method when you want to
1161 apply pressure scaling during data collection, but beware that
1162 you can get very large oscillations if you are starting from a
1163 different pressure. For simulations where the exact fluctation
1164 of the NPT ensemble are important, or if the pressure coupling
1165 time is very short it may not be appropriate, as the previous
1166 time step pressure is used in some steps of the |Gromacs|
1167 implementation for the current time step pressure.
1171 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1172 :mdp-value:`md-vv` or :mdp-value:`md-vv-avek`, very similar to
1173 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1174 time constant :mdp:`tau-p` is the period of pressure
1175 fluctuations at equilibrium. This is probably a better method
1176 when you want to apply pressure scaling during data collection,
1177 but beware that you can get very large oscillations if you are
1178 starting from a different pressure. Currently (as of version
1179 5.1), it only supports isotropic scaling, and only works without
1184 .. mdp-value:: isotropic
1186 Isotropic pressure coupling with time constant
1187 :mdp:`tau-p`. The compressibility and reference pressure are
1188 set with :mdp:`compressibility` and :mdp:`ref-p`, one value is
1191 .. mdp-value:: semiisotropic
1193 Pressure coupling which is isotropic in the ``x`` and ``y``
1194 direction, but different in the ``z`` direction. This can be
1195 useful for membrane simulations. 2 values are needed for ``x/y``
1196 and ``z`` directions respectively.
1198 .. mdp-value:: anisotropic
1200 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1201 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1202 respectively. When the off-diagonal compressibilities are set to
1203 zero, a rectangular box will stay rectangular. Beware that
1204 anisotropic scaling can lead to extreme deformation of the
1207 .. mdp-value:: surface-tension
1209 Surface tension coupling for surfaces parallel to the
1210 xy-plane. Uses normal pressure coupling for the `z`-direction,
1211 while the surface tension is coupled to the `x/y` dimensions of
1212 the box. The first :mdp:`ref-p` value is the reference surface
1213 tension times the number of surfaces ``bar nm``, the second
1214 value is the reference `z`-pressure ``bar``. The two
1215 :mdp:`compressibility` values are the compressibility in the
1216 `x/y` and `z` direction respectively. The value for the
1217 `z`-compressibility should be reasonably accurate since it
1218 influences the convergence of the surface-tension, it can also
1219 be set to zero to have a box with constant height.
1224 The frequency for coupling the pressure. The default value of -1
1225 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1226 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1227 Verlet integrators :mdp:`nstpcouple` is set to 1.
1232 time constant for coupling
1234 .. mdp:: compressibility
1237 compressibility (NOTE: this is now really in bar-1) For water at 1
1238 atm and 300 K the compressibility is 4.5e-5 bar^-1.
1243 reference pressure for coupling
1245 .. mdp:: refcoord-scaling
1249 The reference coordinates for position restraints are not
1250 modified. Note that with this option the virial and pressure
1251 will depend on the absolute positions of the reference
1256 The reference coordinates are scaled with the scaling matrix of
1257 the pressure coupling.
1261 Scale the center of mass of the reference coordinates with the
1262 scaling matrix of the pressure coupling. The vectors of each
1263 reference coordinate to the center of mass are not scaled. Only
1264 one COM is used, even when there are multiple molecules with
1265 position restraints. For calculating the COM of the reference
1266 coordinates in the starting configuration, periodic boundary
1267 conditions are not taken into account.
1273 Simulated annealing is controlled separately for each temperature
1274 group in |Gromacs|. The reference temperature is a piecewise linear
1275 function, but you can use an arbitrary number of points for each
1276 group, and choose either a single sequence or a periodic behaviour for
1277 each group. The actual annealing is performed by dynamically changing
1278 the reference temperature used in the thermostat algorithm selected,
1279 so remember that the system will usually not instantaneously reach the
1280 reference temperature!
1284 Type of annealing for each temperature group
1288 No simulated annealing - just couple to reference temperature value.
1290 .. mdp-value:: single
1292 A single sequence of annealing points. If your simulation is
1293 longer than the time of the last point, the temperature will be
1294 coupled to this constant value after the annealing sequence has
1295 reached the last time point.
1297 .. mdp-value:: periodic
1299 The annealing will start over at the first reference point once
1300 the last reference time is reached. This is repeated until the
1303 .. mdp:: annealing-npoints
1305 A list with the number of annealing reference/control points used
1306 for each temperature group. Use 0 for groups that are not
1307 annealed. The number of entries should equal the number of
1310 .. mdp:: annealing-time
1312 List of times at the annealing reference/control points for each
1313 group. If you are using periodic annealing, the times will be used
1314 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1315 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1316 etc. The number of entries should equal the sum of the numbers
1317 given in :mdp:`annealing-npoints`.
1319 .. mdp:: annealing-temp
1321 List of temperatures at the annealing reference/control points for
1322 each group. The number of entries should equal the sum of the
1323 numbers given in :mdp:`annealing-npoints`.
1325 Confused? OK, let's use an example. Assume you have two temperature
1326 groups, set the group selections to ``annealing = single periodic``,
1327 the number of points of each group to ``annealing-npoints = 3 4``, the
1328 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1329 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1330 will be coupled to 298K at 0ps, but the reference temperature will
1331 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1332 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1333 second group is coupled to 298K at 0ps, it increases linearly to 320K
1334 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1335 decreases to 298K, and then it starts over with the same pattern
1336 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1337 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1347 Do not generate velocities. The velocities are set to zero
1348 when there are no velocities in the input structure file.
1352 Generate velocities in :ref:`gmx grompp` according to a
1353 Maxwell distribution at temperature :mdp:`gen-temp`, with
1354 random seed :mdp:`gen-seed`. This is only meaningful with
1355 integrator :mdp-value:`integrator=md`.
1360 temperature for Maxwell distribution
1365 used to initialize random generator for random velocities,
1366 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1373 .. mdp:: constraints
1377 No constraints except for those defined explicitly in the
1378 topology, *i.e.* bonds are represented by a harmonic (or other)
1379 potential or a Morse potential (depending on the setting of
1380 :mdp:`morse`) and angles by a harmonic (or other) potential.
1382 .. mdp-value:: h-bonds
1384 Convert the bonds with H-atoms to constraints.
1386 .. mdp-value:: all-bonds
1388 Convert all bonds to constraints.
1390 .. mdp-value:: h-angles
1392 Convert all bonds and additionally the angles that involve
1393 H-atoms to bond-constraints.
1395 .. mdp-value:: all-angles
1397 Convert all bonds and angles to bond-constraints.
1399 .. mdp:: constraint-algorithm
1401 .. mdp-value:: LINCS
1403 LINear Constraint Solver. With domain decomposition the parallel
1404 version P-LINCS is used. The accuracy in set with
1405 :mdp:`lincs-order`, which sets the number of matrices in the
1406 expansion for the matrix inversion. After the matrix inversion
1407 correction the algorithm does an iterative correction to
1408 compensate for lengthening due to rotation. The number of such
1409 iterations can be controlled with :mdp:`lincs-iter`. The root
1410 mean square relative constraint deviation is printed to the log
1411 file every :mdp:`nstlog` steps. If a bond rotates more than
1412 :mdp:`lincs-warnangle` in one step, a warning will be printed
1413 both to the log file and to ``stderr``. LINCS should not be used
1414 with coupled angle constraints.
1416 .. mdp-value:: SHAKE
1418 SHAKE is slightly slower and less stable than LINCS, but does
1419 work with angle constraints. The relative tolerance is set with
1420 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1421 does not support constraints between atoms on different nodes,
1422 thus it can not be used with domain decompositon when inter
1423 charge-group constraints are present. SHAKE can not be used with
1424 energy minimization.
1426 .. mdp:: continuation
1428 This option was formerly known as unconstrained-start.
1432 apply constraints to the start configuration and reset shells
1436 do not apply constraints to the start configuration and do not
1437 reset shells, useful for exact coninuation and reruns
1442 relative tolerance for SHAKE
1444 .. mdp:: lincs-order
1447 Highest order in the expansion of the constraint coupling
1448 matrix. When constraints form triangles, an additional expansion of
1449 the same order is applied on top of the normal expansion only for
1450 the couplings within such triangles. For "normal" MD simulations an
1451 order of 4 usually suffices, 6 is needed for large time-steps with
1452 virtual sites or BD. For accurate energy minimization an order of 8
1453 or more might be required. With domain decomposition, the cell size
1454 is limited by the distance spanned by :mdp:`lincs-order` +1
1455 constraints. When one wants to scale further than this limit, one
1456 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1457 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1458 )* :mdp:`lincs-order` remains constant.
1463 Number of iterations to correct for rotational lengthening in
1464 LINCS. For normal runs a single step is sufficient, but for NVE
1465 runs where you want to conserve energy accurately or for accurate
1466 energy minimization you might want to increase it to 2.
1468 .. mdp:: lincs-warnangle
1471 maximum angle that a bond can rotate before LINCS will complain
1477 bonds are represented by a harmonic potential
1481 bonds are represented by a Morse potential
1484 Energy group exclusions
1485 ^^^^^^^^^^^^^^^^^^^^^^^
1487 .. mdp:: energygrp-excl
1489 Pairs of energy groups for which all non-bonded interactions are
1490 excluded. An example: if you have two energy groups ``Protein`` and
1491 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1492 would give only the non-bonded interactions between the protein and
1493 the solvent. This is especially useful for speeding up energy
1494 calculations with ``mdrun -rerun`` and for excluding interactions
1495 within frozen groups.
1504 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1505 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1506 ``=xy``. When set to 2 pressure coupling and Ewald summation can be
1507 used (it is usually best to use semiisotropic pressure coupling
1508 with the ``x/y`` compressibility set to 0, as otherwise the surface
1509 area will change). Walls interact wit the rest of the system
1510 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1511 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1512 monitor the interaction of energy groups with each wall. The center
1513 of mass motion removal will be turned off in the ``z``-direction.
1515 .. mdp:: wall-atomtype
1517 the atom type name in the force field for each wall. By (for
1518 example) defining a special wall atom type in the topology with its
1519 own combination rules, this allows for independent tuning of the
1520 interaction of each atomtype with the walls.
1526 LJ integrated over the volume behind the wall: 9-3 potential
1530 LJ integrated over the wall surface: 10-4 potential
1534 direct LJ potential with the ``z`` distance from the wall
1538 user defined potentials indexed with the ``z`` distance from the
1539 wall, the tables are read analogously to the
1540 :mdp:`energygrp-table` option, where the first name is for a
1541 "normal" energy group and the second name is ``wall0`` or
1542 ``wall1``, only the dispersion and repulsion columns are used
1544 .. mdp:: wall-r-linpot
1547 Below this distance from the wall the potential is continued
1548 linearly and thus the force is constant. Setting this option to a
1549 postive value is especially useful for equilibration when some
1550 atoms are beyond a wall. When the value is <=0 (<0 for
1551 :mdp:`wall-type` =table), a fatal error is generated when atoms
1554 .. mdp:: wall-density
1557 the number density of the atoms for each wall for wall types 9-3
1560 .. mdp:: wall-ewald-zfac
1563 The scaling factor for the third box vector for Ewald summation
1564 only, the minimum is 2. Ewald summation can only be used with
1565 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1566 ``=3dc``. The empty layer in the box serves to decrease the
1567 unphysical Coulomb interaction between periodic images.
1573 Note that where pulling coordinate are applicable, there can be more
1574 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1575 variables will exist accordingly. Documentation references to things
1576 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1577 applicable pulling coordinate.
1583 No center of mass pulling. All the following pull options will
1584 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1589 Center of mass pulling will be applied on 1 or more groups using
1590 1 or more pull coordinates.
1592 .. mdp:: pull-cylinder-r
1595 the radius of the cylinder for
1596 :mdp:`pull-coord1-geometry` = :mdp-value:`cylinder`
1598 .. mdp:: pull-constr-tol
1601 the relative constraint tolerance for constraint pulling
1603 .. mdp:: pull-print-com1
1607 do not print the COM of the first group in each pull coordinate
1611 print the COM of the first group in each pull coordinate
1613 .. mdp:: pull-print-com2
1617 do not print the COM of the second group in each pull coordinate
1621 print the COM of the second group in each pull coordinate
1623 .. mdp:: pull-print-ref-value
1627 do not print the reference value for each pull coordinate
1631 print the reference value for each pull coordinate
1633 .. mdp:: pull-print-components
1637 only print the distance for each pull coordinate
1641 print the distance and Cartesian components selected in
1642 :mdp:`pull-coord1-dim`
1644 .. mdp:: pull-nstxout
1647 frequency for writing out the COMs of all the pull group (0 is
1650 .. mdp:: pull-nstfout
1653 frequency for writing out the force of all the pulled group
1657 .. mdp:: pull-ngroups
1660 The number of pull groups, not including the absolute reference
1661 group, when used. Pull groups can be reused in multiple pull
1662 coordinates. Below only the pull options for group 1 are given,
1663 further groups simply increase the group index number.
1665 .. mdp:: pull-ncoords
1668 The number of pull coordinates. Below only the pull options for
1669 coordinate 1 are given, further coordinates simply increase the
1670 coordinate index number.
1672 .. mdp:: pull-group1-name
1674 The name of the pull group, is looked up in the index file or in
1675 the default groups to obtain the atoms involved.
1677 .. mdp:: pull-group1-weights
1679 Optional relative weights which are multiplied with the masses of
1680 the atoms to give the total weight for the COM. The number should
1681 be 0, meaning all 1, or the number of atoms in the pull group.
1683 .. mdp:: pull-group1-pbcatom
1686 The reference atom for the treatment of periodic boundary
1687 conditions inside the group (this has no effect on the treatment of
1688 the pbc between groups). This option is only important when the
1689 diameter of the pull group is larger than half the shortest box
1690 vector. For determining the COM, all atoms in the group are put at
1691 their periodic image which is closest to
1692 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1693 atom (number wise) is used. This parameter is not used with
1694 :mdp:`pull-group1-geometry` cylinder. A value of -1 turns on cosine
1695 weighting, which is useful for a group of molecules in a periodic
1696 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1699 .. mdp:: pull-coord1-type
1701 .. mdp-value:: umbrella
1703 Center of mass pulling using an umbrella potential between the
1704 reference group and one or more groups.
1706 .. mdp-value:: constraint
1708 Center of mass pulling using a constraint between the reference
1709 group and one or more groups. The setup is identical to the
1710 option umbrella, except for the fact that a rigid constraint is
1711 applied instead of a harmonic potential.
1713 .. mdp-value:: constant-force
1715 Center of mass pulling using a linear potential and therefore a
1716 constant force. For this option there is no reference position
1717 and therefore the parameters :mdp:`pull-coord1-init` and
1718 :mdp:`pull-coord1-rate` are not used.
1720 .. mdp-value:: flat-bottom
1722 At distances beyond :mdp:`pull-coord1-init` a harmonic potential
1723 is applied, otherwise no potential is applied.
1725 .. mdp:: pull-coord1-geometry
1727 .. mdp-value:: distance
1729 Pull along the vector connecting the two groups. Components can
1730 be selected with :mdp:`pull-coord1-dim`.
1732 .. mdp-value:: direction
1734 Pull in the direction of :mdp:`pull-coord1-vec`.
1736 .. mdp-value:: direction-periodic
1738 As :mdp-value:`direction`, but allows the distance to be larger
1739 than half the box size. With this geometry the box should not be
1740 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1741 the pull force is not added to virial.
1743 .. mdp-value:: direction-relative
1745 As :mdp-value:`direction`, but the pull vector is the vector
1746 that points from the COM of a third to the COM of a fourth pull
1747 group. This means that 4 groups need to be supplied in
1748 :mdp:`pull-coord1-groups`. Note that the pull force will give
1749 rise to a torque on the pull vector, which is turn leads to
1750 forces perpendicular to the pull vector on the two groups
1751 defining the vector. If you want a pull group to move between
1752 the two groups defining the vector, simply use the union of
1753 these two groups as the reference group.
1755 .. mdp-value:: cylinder
1757 Designed for pulling with respect to a layer where the reference
1758 COM is given by a local cylindrical part of the reference group.
1759 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1760 the first of the two groups in :mdp:`pull-coord1-groups` a
1761 cylinder is selected around the axis going through the COM of
1762 the second group with direction :mdp:`pull-coord1-vec` with
1763 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1764 continously to zero as the radial distance goes from 0 to
1765 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1766 dependence gives rise to radial forces on both pull groups.
1767 Note that the radius should be smaller than half the box size.
1768 For tilted cylinders they should be even smaller than half the
1769 box size since the distance of an atom in the reference group
1770 from the COM of the pull group has both a radial and an axial
1771 component. This geometry is not supported with constraint
1774 .. mdp:: pull-coord1-groups
1776 The two groups indices should be given on which this pull
1777 coordinate will operate. The first index can be 0, in which case an
1778 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1779 absolute reference the system is no longer translation invariant
1780 and one should think about what to do with the center of mass
1781 motion. Note that (only) for :mdp:`pull-coord1-geometry` =
1782 :mdp-value:`direction-relative` four groups are required.
1784 .. mdp:: pull-coord1-dim
1787 Selects the dimensions that this pull coordinate acts on and that
1788 are printed to the output files when
1789 :mdp:`pull-print-components` = :mdp-value:`yes`. With
1790 :mdp:`pull-coord1-geometry` = :mdp-value:`distance`, only Cartesian
1791 components set to Y contribute to the distance. Thus setting this
1792 to Y Y N results in a distance in the x/y plane. With other
1793 geometries all dimensions with non-zero entries in
1794 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1795 dimensions only affect the output.
1797 .. mdp:: pull-coord1-origin
1800 The pull reference position for use with an absolute reference.
1802 .. mdp:: pull-coord1-vec
1805 The pull direction. :ref:`gmx grompp` normalizes the vector.
1807 .. mdp:: pull-coord1-start
1811 do not modify :mdp:`pull-coord1-init`
1815 add the COM distance of the starting conformation to
1816 :mdp:`pull-coord1-init`
1818 .. mdp:: pull-coord1-init
1821 The reference distance at t=0.
1823 .. mdp:: pull-coord1-rate
1826 The rate of change of the reference position.
1828 .. mdp:: pull-coord1-k
1830 (0) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\]
1831 The force constant. For umbrella pulling this is the harmonic force
1832 constant in kJ mol-1 nm-2. For constant force pulling this is the
1833 force constant of the linear potential, and thus the negative (!)
1834 of the constant force in kJ mol-1 nm-1.
1836 .. mdp:: pull-coord1-kB
1838 (pull-k1) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\]
1839 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1840 :mdp:`free-energy` is turned on. The force constant is then (1 -
1841 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1851 ignore distance restraint information in topology file
1853 .. mdp-value:: simple
1855 simple (per-molecule) distance restraints.
1857 .. mdp-value:: ensemble
1859 distance restraints over an ensemble of molecules in one
1860 simulation box. Normally, one would perform ensemble averaging
1861 over multiple subsystems, each in a separate box, using ``mdrun
1862 -multi``. Supply ``topol0.tpr``, ``topol1.tpr``, ... with
1863 different coordinates and/or velocities. The environment
1864 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
1865 within each ensemble (usually equal to the ``mdrun -multi``
1868 .. mdp:: disre-weighting
1870 .. mdp-value:: equal
1872 divide the restraint force equally over all atom pairs in the
1875 .. mdp-value:: conservative
1877 the forces are the derivative of the restraint potential, this
1878 results in an weighting of the atom pairs to the reciprocal
1879 seventh power of the displacement. The forces are conservative
1880 when :mdp:`disre-tau` is zero.
1882 .. mdp:: disre-mixed
1886 the violation used in the calculation of the restraint force is
1887 the time-averaged violation
1891 the violation used in the calculation of the restraint force is
1892 the square root of the product of the time-averaged violation
1893 and the instantaneous violation
1897 (1000) \[kJ mol-1 nm-2\]
1898 force constant for distance restraints, which is multiplied by a
1899 (possibly) different factor for each restraint given in the `fac`
1900 column of the interaction in the topology file.
1905 time constant for distance restraints running average. A value of
1906 zero turns off time averaging.
1908 .. mdp:: nstdisreout
1911 period between steps when the running time-averaged and
1912 instantaneous distances of all atom pairs involved in restraints
1913 are written to the energy file (can make the energy file very
1920 ignore orientation restraint information in topology file
1924 use orientation restraints, ensemble averaging can be performed
1930 force constant for orientation restraints, which is multiplied by a
1931 (possibly) different weight factor for each restraint, can be set
1932 to zero to obtain the orientations from a free simulation
1937 time constant for orientation restraints running average. A value
1938 of zero turns off time averaging.
1940 .. mdp:: orire-fitgrp
1942 fit group for orientation restraining. This group of atoms is used
1943 to determine the rotation **R** of the system with respect to the
1944 reference orientation. The reference orientation is the starting
1945 conformation of the first subsystem. For a protein, backbone is a
1948 .. mdp:: nstorireout
1951 period between steps when the running time-averaged and
1952 instantaneous orientations for all restraints, and the molecular
1953 order tensor are written to the energy file (can make the energy
1957 Free energy calculations
1958 ^^^^^^^^^^^^^^^^^^^^^^^^
1960 .. mdp:: free-energy
1964 Only use topology A.
1968 Interpolate between topology A (lambda=0) to topology B
1969 (lambda=1) and write the derivative of the Hamiltonian with
1970 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
1971 or the Hamiltonian differences with respect to other lambda
1972 values (as specified with foreign lambda) to the energy file
1973 and/or to ``dhdl.xvg``, where they can be processed by, for
1974 example :ref:`gmx bar`. The potentials, bond-lengths and angles
1975 are interpolated linearly as described in the manual. When
1976 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
1977 used for the LJ and Coulomb interactions.
1981 Turns on expanded ensemble simulation, where the alchemical state
1982 becomes a dynamic variable, allowing jumping between different
1983 Hamiltonians. See the expanded ensemble options for controlling how
1984 expanded ensemble simulations are performed. The different
1985 Hamiltonians used in expanded ensemble simulations are defined by
1986 the other free energy options.
1988 .. mdp:: init-lambda
1991 starting value for lambda (float). Generally, this should only be
1992 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
1993 other cases, :mdp:`init-lambda-state` should be specified
1994 instead. Must be greater than or equal to 0.
1996 .. mdp:: delta-lambda
1999 increment per time step for lambda
2001 .. mdp:: init-lambda-state
2004 starting value for the lambda state (integer). Specifies which
2005 columm of the lambda vector (:mdp:`coul-lambdas`,
2006 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2007 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2008 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2009 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2010 the first column, and so on.
2012 .. mdp:: fep-lambdas
2015 Zero, one or more lambda values for which Delta H values will be
2016 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2017 steps. Values must be between 0 and 1. Free energy differences
2018 between different lambda values can then be determined with
2019 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2020 other -lambdas keywords because all components of the lambda vector
2021 that are not specified will use :mdp:`fep-lambdas` (including
2022 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2024 .. mdp:: coul-lambdas
2027 Zero, one or more lambda values for which Delta H values will be
2028 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2029 steps. Values must be between 0 and 1. Only the electrostatic
2030 interactions are controlled with this component of the lambda
2031 vector (and only if the lambda=0 and lambda=1 states have differing
2032 electrostatic interactions).
2034 .. mdp:: vdw-lambdas
2037 Zero, one or more lambda values for which Delta H values will be
2038 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2039 steps. Values must be between 0 and 1. Only the van der Waals
2040 interactions are controlled with this component of the lambda
2043 .. mdp:: bonded-lambdas
2046 Zero, one or more lambda values for which Delta H values will be
2047 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2048 steps. Values must be between 0 and 1. Only the bonded interactions
2049 are controlled with this component of the lambda vector.
2051 .. mdp:: restraint-lambdas
2054 Zero, one or more lambda values for which Delta H values will be
2055 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2056 steps. Values must be between 0 and 1. Only the restraint
2057 interactions: dihedral restraints, and the pull code restraints are
2058 controlled with this component of the lambda vector.
2060 .. mdp:: mass-lambdas
2063 Zero, one or more lambda values for which Delta H values will be
2064 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2065 steps. Values must be between 0 and 1. Only the particle masses are
2066 controlled with this component of the lambda vector.
2068 .. mdp:: temperature-lambdas
2071 Zero, one or more lambda values for which Delta H values will be
2072 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2073 steps. Values must be between 0 and 1. Only the temperatures
2074 controlled with this component of the lambda vector. Note that
2075 these lambdas should not be used for replica exchange, only for
2076 simulated tempering.
2078 .. mdp:: calc-lambda-neighbors
2081 Controls the number of lambda values for which Delta H values will
2082 be calculated and written out, if :mdp:`init-lambda-state` has
2083 been set. A positive value will limit the number of lambda points
2084 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2085 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2086 has a value of 2, energies for lambda points 3-7 will be calculated
2087 and writen out. A value of -1 means all lambda points will be
2088 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2089 1 is sufficient, while for MBAR -1 should be used.
2094 the soft-core alpha parameter, a value of 0 results in linear
2095 interpolation of the LJ and Coulomb interactions
2100 the power of the radial term in the soft-core equation. Possible
2101 values are 6 and 48. 6 is more standard, and is the default. When
2102 48 is used, then sc-alpha should generally be much lower (between
2108 Whether to apply the soft-core free energy interaction
2109 transformation to the Columbic interaction of a molecule. Default
2110 is no, as it is generally more efficient to turn off the Coulomic
2111 interactions linearly before turning off the van der Waals
2112 interactions. Note that it is only taken into account when lambda
2113 states are used, not with :mdp:`couple-lambda0` /
2114 :mdp:`couple-lambda1`, and you can still turn off soft-core
2115 interactions by setting :mdp:`sc-alpha` to 0.
2120 the power for lambda in the soft-core function, only the values 1
2126 the soft-core sigma for particles which have a C6 or C12 parameter
2127 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2129 .. mdp:: couple-moltype
2131 Here one can supply a molecule type (as defined in the topology)
2132 for calculating solvation or coupling free energies. There is a
2133 special option ``system`` that couples all molecule types in the
2134 system. This can be useful for equilibrating a system starting from
2135 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2136 on. The Van der Waals interactions and/or charges in this molecule
2137 type can be turned on or off between lambda=0 and lambda=1,
2138 depending on the settings of :mdp:`couple-lambda0` and
2139 :mdp:`couple-lambda1`. If you want to decouple one of several
2140 copies of a molecule, you need to copy and rename the molecule
2141 definition in the topology.
2143 .. mdp:: couple-lambda0
2145 .. mdp-value:: vdw-q
2147 all interactions are on at lambda=0
2151 the charges are zero (no Coulomb interactions) at lambda=0
2155 the Van der Waals interactions are turned at lambda=0; soft-core
2156 interactions will be required to avoid singularities
2160 the Van der Waals interactions are turned off and the charges
2161 are zero at lambda=0; soft-core interactions will be required to
2162 avoid singularities.
2164 .. mdp:: couple-lambda1
2166 analogous to :mdp:`couple-lambda1`, but for lambda=1
2168 .. mdp:: couple-intramol
2172 All intra-molecular non-bonded interactions for moleculetype
2173 :mdp:`couple-moltype` are replaced by exclusions and explicit
2174 pair interactions. In this manner the decoupled state of the
2175 molecule corresponds to the proper vacuum state without
2176 periodicity effects.
2180 The intra-molecular Van der Waals and Coulomb interactions are
2181 also turned on/off. This can be useful for partitioning
2182 free-energies of relatively large molecules, where the
2183 intra-molecular non-bonded interactions might lead to
2184 kinetically trapped vacuum conformations. The 1-4 pair
2185 interactions are not turned off.
2190 the frequency for writing dH/dlambda and possibly Delta H to
2191 dhdl.xvg, 0 means no ouput, should be a multiple of
2192 :mdp:`nstcalcenergy`.
2194 .. mdp:: dhdl-derivatives
2198 If yes (the default), the derivatives of the Hamiltonian with
2199 respect to lambda at each :mdp:`nstdhdl` step are written
2200 out. These values are needed for interpolation of linear energy
2201 differences with :ref:`gmx bar` (although the same can also be
2202 achieved with the right foreign lambda setting, that may not be as
2203 flexible), or with thermodynamic integration
2205 .. mdp:: dhdl-print-energy
2209 Include either the total or the potential energy in the dhdl
2210 file. Options are 'no', 'potential', or 'total'. This information
2211 is needed for later free energy analysis if the states of interest
2212 are at different temperatures. If all states are at the same
2213 temperature, this information is not needed. 'potential' is useful
2214 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2215 file. When rerunning from an existing trajectory, the kinetic
2216 energy will often not be correct, and thus one must compute the
2217 residual free energy from the potential alone, with the kinetic
2218 energy component computed analytically.
2220 .. mdp:: separate-dhdl-file
2224 The free energy values that are calculated (as specified with
2225 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2226 written out to a separate file, with the default name
2227 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2232 The free energy values are written out to the energy output file
2233 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2234 steps), where they can be extracted with :ref:`gmx energy` or
2235 used directly with :ref:`gmx bar`.
2237 .. mdp:: dh-hist-size
2240 If nonzero, specifies the size of the histogram into which the
2241 Delta H values (specified with foreign lambda) and the derivative
2242 dH/dl values are binned, and written to ener.edr. This can be used
2243 to save disk space while calculating free energy differences. One
2244 histogram gets written for each foreign lambda and two for the
2245 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2246 histogram settings (too small size or too wide bins) can introduce
2247 errors. Do not use histograms unless you're certain you need it.
2249 .. mdp:: dh-hist-spacing
2252 Specifies the bin width of the histograms, in energy units. Used in
2253 conjunction with :mdp:`dh-hist-size`. This size limits the
2254 accuracy with which free energies can be calculated. Do not use
2255 histograms unless you're certain you need it.
2258 Expanded Ensemble calculations
2259 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2261 .. mdp:: nstexpanded
2263 The number of integration steps beween attempted moves changing the
2264 system Hamiltonian in expanded ensemble simulations. Must be a
2265 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2272 No Monte Carlo in state space is performed.
2274 .. mdp-value:: metropolis-transition
2276 Uses the Metropolis weights to update the expanded ensemble
2277 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2280 .. mdp-value:: barker-transition
2282 Uses the Barker transition critera to update the expanded
2283 ensemble weight of each state i, defined by exp(-beta_new
2284 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2286 .. mdp-value:: wang-landau
2288 Uses the Wang-Landau algorithm (in state space, not energy
2289 space) to update the expanded ensemble weights.
2291 .. mdp-value:: min-variance
2293 Uses the minimum variance updating method of Escobedo et al. to
2294 update the expanded ensemble weights. Weights will not be the
2295 free energies, but will rather emphasize states that need more
2296 sampling to give even uncertainty.
2298 .. mdp:: lmc-mc-move
2302 No Monte Carlo in state space is performed.
2304 .. mdp-value:: metropolis-transition
2306 Randomly chooses a new state up or down, then uses the
2307 Metropolis critera to decide whether to accept or reject:
2308 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2310 .. mdp-value:: barker-transition
2312 Randomly chooses a new state up or down, then uses the Barker
2313 transition critera to decide whether to accept or reject:
2314 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2316 .. mdp-value:: gibbs
2318 Uses the conditional weights of the state given the coordinate
2319 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2322 .. mdp-value:: metropolized-gibbs
2324 Uses the conditional weights of the state given the coordinate
2325 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2326 to move to, EXCLUDING the current state, then uses a rejection
2327 step to ensure detailed balance. Always more efficient that
2328 Gibbs, though only marginally so in many situations, such as
2329 when only the nearest neighbors have decent phase space
2335 random seed to use for Monte Carlo moves in state space. When
2336 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2338 .. mdp:: mc-temperature
2340 Temperature used for acceptance/rejection for Monte Carlo moves. If
2341 not specified, the temperature of the simulation specified in the
2342 first group of :mdp:`ref-t` is used.
2347 The cutoff for the histogram of state occupancies to be reset, and
2348 the free energy incrementor to be changed from delta to delta *
2349 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2350 each histogram) / (average number of samples at each
2351 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2352 histogram is only considered flat if all Nratio > 0.8 AND
2353 simultaneously all 1/Nratio > 0.8.
2358 Each time the histogram is considered flat, then the current value
2359 of the Wang-Landau incrementor for the free energies is multiplied
2360 by :mdp:`wl-scale`. Value must be between 0 and 1.
2362 .. mdp:: init-wl-delta
2365 The initial value of the Wang-Landau incrementor in kT. Some value
2366 near 1 kT is usually most efficient, though sometimes a value of
2367 2-3 in units of kT works better if the free energy differences are
2370 .. mdp:: wl-oneovert
2373 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2374 the large sample limit. There is significant evidence that the
2375 standard Wang-Landau algorithms in state space presented here
2376 result in free energies getting 'burned in' to incorrect values
2377 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2378 then when the incrementor becomes less than 1/N, where N is the
2379 mumber of samples collected (and thus proportional to the data
2380 collection time, hence '1 over t'), then the Wang-Lambda
2381 incrementor is set to 1/N, decreasing every step. Once this occurs,
2382 :mdp:`wl-ratio` is ignored, but the weights will still stop
2383 updating when the equilibration criteria set in
2384 :mdp:`lmc-weights-equil` is achieved.
2386 .. mdp:: lmc-repeats
2389 Controls the number of times that each Monte Carlo swap type is
2390 performed each iteration. In the limit of large numbers of Monte
2391 Carlo repeats, then all methods converge to Gibbs sampling. The
2392 value will generally not need to be different from 1.
2394 .. mdp:: lmc-gibbsdelta
2397 Limit Gibbs sampling to selected numbers of neighboring states. For
2398 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2399 sampling over all of the states that are defined. A positive value
2400 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2401 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2402 value of -1 means that all states are considered. For less than 100
2403 states, it is probably not that expensive to include all states.
2405 .. mdp:: lmc-forced-nstart
2408 Force initial state space sampling to generate weights. In order to
2409 come up with reasonable initial weights, this setting allows the
2410 simulation to drive from the initial to the final lambda state,
2411 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2412 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2413 sufficiently long (thousands of steps, perhaps), then the weights
2414 will be close to correct. However, in most cases, it is probably
2415 better to simply run the standard weight equilibration algorithms.
2417 .. mdp:: nst-transition-matrix
2420 Frequency of outputting the expanded ensemble transition matrix. A
2421 negative number means it will only be printed at the end of the
2424 .. mdp:: symmetrized-transition-matrix
2427 Whether to symmetrize the empirical transition matrix. In the
2428 infinite limit the matrix will be symmetric, but will diverge with
2429 statistical noise for short timescales. Forced symmetrization, by
2430 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2431 like the existence of (small magnitude) negative eigenvalues.
2433 .. mdp:: mininum-var-min
2436 The min-variance strategy (option of :mdp:`lmc-stats` is only
2437 valid for larger number of samples, and can get stuck if too few
2438 samples are used at each state. :mdp:`mininum-var-min` is the
2439 minimum number of samples that each state that are allowed before
2440 the min-variance strategy is activated if selected.
2442 .. mdp:: init-lambda-weights
2444 The initial weights (free energies) used for the expanded ensemble
2445 states. Default is a vector of zero weights. format is similar to
2446 the lambda vector settings in :mdp:`fep-lambdas`, except the
2447 weights can be any floating point number. Units are kT. Its length
2448 must match the lambda vector lengths.
2450 .. mdp:: lmc-weights-equil
2454 Expanded ensemble weights continue to be updated throughout the
2459 The input expanded ensemble weights are treated as equilibrated,
2460 and are not updated throughout the simulation.
2462 .. mdp-value:: wl-delta
2464 Expanded ensemble weight updating is stopped when the
2465 Wang-Landau incrementor falls below this value.
2467 .. mdp-value:: number-all-lambda
2469 Expanded ensemble weight updating is stopped when the number of
2470 samples at all of the lambda states is greater than this value.
2472 .. mdp-value:: number-steps
2474 Expanded ensemble weight updating is stopped when the number of
2475 steps is greater than the level specified by this value.
2477 .. mdp-value:: number-samples
2479 Expanded ensemble weight updating is stopped when the number of
2480 total samples across all lambda states is greater than the level
2481 specified by this value.
2483 .. mdp-value:: count-ratio
2485 Expanded ensemble weight updating is stopped when the ratio of
2486 samples at the least sampled lambda state and most sampled
2487 lambda state greater than this value.
2489 .. mdp:: simulated-tempering
2492 Turn simulated tempering on or off. Simulated tempering is
2493 implemented as expanded ensemble sampling with different
2494 temperatures instead of different Hamiltonians.
2496 .. mdp:: sim-temp-low
2499 Low temperature for simulated tempering.
2501 .. mdp:: sim-temp-high
2504 High temperature for simulated tempering.
2506 .. mdp:: simulated-tempering-scaling
2508 Controls the way that the temperatures at intermediate lambdas are
2509 calculated from the :mdp:`temperature-lambdas` part of the lambda
2512 .. mdp-value:: linear
2514 Linearly interpolates the temperatures using the values of
2515 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2516 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2517 a temperature of 350. A nonlinear set of temperatures can always
2518 be implemented with uneven spacing in lambda.
2520 .. mdp-value:: geometric
2522 Interpolates temperatures geometrically between
2523 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2524 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2525 :mdp:`sim-temp-low`) raised to the power of
2526 (i/(ntemps-1)). This should give roughly equal exchange for
2527 constant heat capacity, though of course things simulations that
2528 involve protein folding have very high heat capacity peaks.
2530 .. mdp-value:: exponential
2532 Interpolates temperatures exponentially between
2533 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2534 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2535 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2536 (i))-1)/(exp(1.0)-i)).
2544 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2545 in groups Protein and Sol will experience constant acceleration as
2546 specified in the :mdp:`accelerate` line
2551 acceleration for :mdp:`acc-grps`; x, y and z for each group
2552 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2553 constant acceleration of 0.1 nm ps-2 in X direction, second group
2558 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2559 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2560 specifies for which dimension the freezing applies. To avoid
2561 spurious contibrutions to the virial and pressure due to large
2562 forces between completely frozen atoms you need to use energy group
2563 exclusions, this also saves computing time. Note that coordinates
2564 of frozen atoms are not scaled by pressure-coupling algorithms.
2568 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2569 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
2570 N N N N`` means that particles in the first group can move only in
2571 Z direction. The particles in the second group can move in any
2574 .. mdp:: cos-acceleration
2577 the amplitude of the acceleration profile for calculating the
2578 viscosity. The acceleration is in the X-direction and the magnitude
2579 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2580 added to the energy file: the amplitude of the velocity profile and
2585 (0 0 0 0 0 0) \[nm ps-1\]
2586 The velocities of deformation for the box elements: a(x) b(y) c(z)
2587 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2588 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2589 elements are corrected for periodicity. The coordinates are
2590 transformed accordingly. Frozen degrees of freedom are (purposely)
2591 also transformed. The time ts is set to t at the first step and at
2592 steps at which x and v are written to trajectory to ensure exact
2593 restarts. Deformation can be used together with semiisotropic or
2594 anisotropic pressure coupling when the appropriate
2595 compressibilities are set to zero. The diagonal elements can be
2596 used to strain a solid. The off-diagonal elements can be used to
2597 shear a solid or a liquid.
2603 .. mdp:: E-x ; E-y ; E-z
2605 If you want to use an electric field in a direction, enter 3
2606 numbers after the appropriate E-direction, the first number: the
2607 number of cosines, only 1 is implemented (with frequency 0) so
2608 enter 1, the second number: the strength of the electric field in V
2609 nm^-1, the third number: the phase of the cosine, you can enter any
2610 number here since a cosine of frequency zero has no phase.
2612 .. mdp:: E-xt; E-yt; E-zt
2614 Here you can specify a pulsed alternating electric field. The field
2615 has the form of a gaussian laser pulse:
2617 E(t) = E0 exp ( -(t-t0)^2/(2 sigma^2) ) cos(omega (t-t0))
2619 For example, the four parameters for direction x are set in the
2620 three fields of :mdp:`E-x` and :mdp:`E-xt` like
2624 E-xt = omega t0 sigma
2626 In the special case that sigma = 0, the exponential term is omitted
2627 and only the cosine term is used.
2629 More details in Carl Caleman and David van der Spoel: Picosecond
2630 Melting of Ice by an Infrared Laser Pulse - A Simulation Study
2631 Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008)
2635 Mixed quantum/classical molecular dynamics
2636 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2646 Do a QM/MM simulation. Several groups can be described at
2647 different QM levels separately. These are specified in the
2648 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
2649 initio* theory at which the groups are described is specified by
2650 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
2651 groups at different levels of theory is only possible with the
2652 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
2656 groups to be descibed at the QM level
2660 .. mdp-value:: normal
2662 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
2663 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
2664 *ab initio* theory. The rest of the system is described at the
2665 MM level. The QM and MM subsystems interact as follows: MM point
2666 charges are included in the QM one-electron hamiltonian and all
2667 Lennard-Jones interactions are described at the MM level.
2669 .. mdp-value:: ONIOM
2671 The interaction between the subsystem is described using the
2672 ONIOM method by Morokuma and co-workers. There can be more than
2673 one :mdp:`QMMM-grps` each modeled at a different level of QM
2674 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
2679 Method used to compute the energy and gradients on the QM
2680 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
2681 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
2682 included in the active space is specified by :mdp:`CASelectrons`
2683 and :mdp:`CASorbitals`.
2688 Basis set used to expand the electronic wavefuntion. Only Gaussian
2689 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
2690 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
2695 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
2696 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
2697 layer needs to be specified separately.
2702 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
2703 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
2704 needs to be specified separately.
2706 .. mdp:: CASorbitals
2709 The number of orbitals to be included in the active space when
2710 doing a CASSCF computation.
2712 .. mdp:: CASelectrons
2715 The number of electrons to be included in the active space when
2716 doing a CASSCF computation.
2722 No surface hopping. The system is always in the electronic
2727 Do a QM/MM MD simulation on the excited state-potential energy
2728 surface and enforce a *diabatic* hop to the ground-state when
2729 the system hits the conical intersection hyperline in the course
2730 the simulation. This option only works in combination with the
2737 .. mdp:: implicit-solvent
2745 Do a simulation with implicit solvent using the Generalized Born
2746 formalism. Three different methods for calculating the Born
2747 radii are available, Still, HCT and OBC. These are specified
2748 with the :mdp:`gb-algorithm` field. The non-polar solvation is
2749 specified with the :mdp:`sa-algorithm` field.
2751 .. mdp:: gb-algorithm
2753 .. mdp-value:: Still
2755 Use the Still method to calculate the Born radii
2759 Use the Hawkins-Cramer-Truhlar method to calculate the Born
2764 Use the Onufriev-Bashford-Case method to calculate the Born
2770 Frequency to (re)-calculate the Born radii. For most practial
2771 purposes, setting a value larger than 1 violates energy
2772 conservation and leads to unstable trajectories.
2777 Cut-off for the calculation of the Born radii. Currently must be
2780 .. mdp:: gb-epsilon-solvent
2783 Dielectric constant for the implicit solvent
2785 .. mdp:: gb-saltconc
2788 Salt concentration for implicit solvent models, currently not used
2790 .. mdp:: gb-obc-alpha
2791 .. mdp:: gb-obc-beta
2792 .. mdp:: gb-obc-gamma
2794 Scale factors for the OBC model. Default values of 1, 0.78 and 4.85
2795 respectively are for OBC(II). Values for OBC(I) are 0.8, 0 and 2.91
2798 .. mdp:: gb-dielectric-offset
2801 Distance for the di-electric offset when calculating the Born
2802 radii. This is the offset between the center of each atom the
2803 center of the polarization energy for the corresponding atom
2805 .. mdp:: sa-algorithm
2807 .. mdp-value:: Ace-approximation
2809 Use an Ace-type approximation
2813 No non-polar solvation calculation done. For GBSA only the polar
2814 part gets calculated
2816 .. mdp:: sa-surface-tension
2819 Default value for surface tension with SA algorithms. The default
2820 value is -1; Note that if this default value is not changed it will
2821 be overridden by :ref:`gmx grompp` using values that are specific
2822 for the choice of radii algorithm (0.0049 kcal/mol/Angstrom^2 for
2823 Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will
2824 while using an sa-algorithm other than None means no non-polar
2825 calculations are done.
2828 Adaptive Resolution Simulation
2829 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2834 Decide whether the AdResS feature is turned on.
2836 .. mdp:: adress-type
2840 Do an AdResS simulation with weight equal 1, which is equivalent
2841 to an explicit (normal) MD simulation. The difference to
2842 disabled AdResS is that the AdResS variables are still read-in
2843 and hence are defined.
2845 .. mdp-value:: Constant
2847 Do an AdResS simulation with a constant weight,
2848 :mdp:`adress-const-wf` defines the value of the weight
2850 .. mdp-value:: XSplit
2852 Do an AdResS simulation with simulation box split in
2853 x-direction, so basically the weight is only a function of the x
2854 coordinate and all distances are measured using the x coordinate
2857 .. mdp-value:: Sphere
2859 Do an AdResS simulation with spherical explicit zone.
2861 .. mdp:: adress-const-wf
2864 Provides the weight for a constant weight simulation
2865 (:mdp:`adress-type` =Constant)
2867 .. mdp:: adress-ex-width
2870 Width of the explicit zone, measured from
2871 :mdp:`adress-reference-coords`.
2873 .. mdp:: adress-hy-width
2876 Width of the hybrid zone.
2878 .. mdp:: adress-reference-coords
2881 Position of the center of the explicit zone. Periodic boundary
2882 conditions apply for measuring the distance from it.
2884 .. mdp:: adress-cg-grp-names
2886 The names of the coarse-grained energy groups. All other energy
2887 groups are considered explicit and their interactions will be
2888 automatically excluded with the coarse-grained groups.
2890 .. mdp:: adress-site
2892 The mapping point from which the weight is calculated.
2896 The weight is calculated from the center of mass of each charge group.
2900 The weight is calculated from the center of geometry of each charge group.
2904 The weight is calculated from the position of 1st atom of each charge group.
2906 .. mdp-value:: AtomPerAtom
2908 The weight is calculated from the position of each individual atom.
2910 .. mdp:: adress-interface-correction
2914 Do not apply any interface correction.
2916 .. mdp-value:: thermoforce
2918 Apply thermodynamic force interface correction. The table can be
2919 specified using the ``-tabletf`` option of :ref:`gmx mdrun`. The
2920 table should contain the potential and force (acting on
2921 molecules) as function of the distance from
2922 :mdp:`adress-reference-coords`.
2924 .. mdp:: adress-tf-grp-names
2926 The names of the energy groups to which the thermoforce is applied
2927 if enabled in :mdp:`adress-interface-correction`. If no group is
2928 given the default table is applied.
2930 .. mdp:: adress-ex-forcecap
2933 Cap the force in the hybrid region, useful for big molecules. 0
2934 disables force capping.
2937 User defined thingies
2938 ^^^^^^^^^^^^^^^^^^^^^
2942 .. mdp:: userint1 (0)
2943 .. mdp:: userint2 (0)
2944 .. mdp:: userint3 (0)
2945 .. mdp:: userint4 (0)
2946 .. mdp:: userreal1 (0)
2947 .. mdp:: userreal2 (0)
2948 .. mdp:: userreal3 (0)
2949 .. mdp:: userreal4 (0)
2951 These you can use if you modify code. You can pass integers and
2952 reals and groups to your subroutine. Check the inputrec definition
2953 in ``src/gromacs/legacyheaders/types/inputrec.h``
2955 .. _reference manual: gmx-manual-parent-dir_