2 See the "run control" section for a working example of the
3 syntax to use when making .mdp entries, with and without detailed
4 documentation for values those entries might take. Everything can
5 be cross-referenced, see the examples there. TODO Make more
8 Molecular dynamics parameters (.mdp options)
9 ============================================
16 Default values are given in parentheses, or listed first among
17 choices. The first option in the list is always the default
18 option. Units are given in square brackets. The difference between a
19 dash and an underscore is ignored.
21 A :ref:`sample mdp file <mdp>` is available. This should be
22 appropriate to start a normal simulation. Edit it to suit your
23 specific needs and desires.
31 directories to include in your topology. Format:
32 ``-I/home/john/mylib -I../otherlib``
36 defines to pass to the preprocessor, default is no defines. You can
37 use any defines to control options in your customized topology
38 files. Options that act on existing :ref:`top` file mechanisms
41 ``-DFLEXIBLE`` will use flexible water instead of rigid water
42 into your topology, this can be useful for normal mode analysis.
44 ``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
45 your topology, used for implementing position restraints.
53 (Despite the name, this list includes algorithms that are not
54 actually integrators over time. :mdp-value:`integrator=steep` and
55 all entries following it are in this category)
59 A leap-frog algorithm for integrating Newton's equations of motion.
63 A velocity Verlet algorithm for integrating Newton's equations
64 of motion. For constant NVE simulations started from
65 corresponding points in the same trajectory, the trajectories
66 are analytically, but not binary, identical to the
67 :mdp-value:`integrator=md` leap-frog integrator. The the kinetic
68 energy, which is determined from the whole step velocities and
69 is therefore slightly too high. The advantage of this integrator
70 is more accurate, reversible Nose-Hoover and Parrinello-Rahman
71 coupling integration based on Trotter expansion, as well as
72 (slightly too small) full step velocity output. This all comes
73 at the cost off extra computation, especially with constraints
74 and extra communication in parallel. Note that for nearly all
75 production simulations the :mdp-value:`integrator=md` integrator
78 .. mdp-value:: md-vv-avek
80 A velocity Verlet algorithm identical to
81 :mdp-value:`integrator=md-vv`, except that the kinetic energy is
82 determined as the average of the two half step kinetic energies
83 as in the :mdp-value:`integrator=md` integrator, and this thus
84 more accurate. With Nose-Hoover and/or Parrinello-Rahman
85 coupling this comes with a slight increase in computational
90 An accurate and efficient leap-frog stochastic dynamics
91 integrator. With constraints, coordinates needs to be
92 constrained twice per integration step. Depending on the
93 computational cost of the force calculation, this can take a
94 significant part of the simulation time. The temperature for one
95 or more groups of atoms (:mdp:`tc-grps`) is set with
96 :mdp:`ref-t`, the inverse friction constant for each group is
97 set with :mdp:`tau-t`. The parameter :mdp:`tcoupl` is
98 ignored. The random generator is initialized with
99 :mdp:`ld-seed`. When used as a thermostat, an appropriate value
100 for :mdp:`tau-t` is 2 ps, since this results in a friction that
101 is lower than the internal friction of water, while it is high
102 enough to remove excess heat NOTE: temperature deviations decay
103 twice as fast as with a Berendsen thermostat with the same
108 An Euler integrator for Brownian or position Langevin dynamics,
109 the velocity is the force divided by a friction coefficient
110 (:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
111 :mdp:`bd-fric` is 0, the friction coefficient for each particle
112 is calculated as mass/ :mdp:`tau-t`, as for the integrator
113 :mdp-value:`integrator=sd`. The random generator is initialized
118 A steepest descent algorithm for energy minimization. The
119 maximum step size is :mdp:`emstep`, the tolerance is
124 A conjugate gradient algorithm for energy minimization, the
125 tolerance is :mdp:`emtol`. CG is more efficient when a steepest
126 descent step is done every once in a while, this is determined
127 by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
128 analysis, which requires a very high accuracy, |Gromacs| should be
129 compiled in double precision.
131 .. mdp-value:: l-bfgs
133 A quasi-Newtonian algorithm for energy minimization according to
134 the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
135 practice this seems to converge faster than Conjugate Gradients,
136 but due to the correction steps necessary it is not (yet)
141 Normal mode analysis is performed on the structure in the :ref:`tpr`
142 file. |Gromacs| should be compiled in double precision.
146 Test particle insertion. The last molecule in the topology is
147 the test particle. A trajectory must be provided to ``mdrun
148 -rerun``. This trajectory should not contain the molecule to be
149 inserted. Insertions are performed :mdp:`nsteps` times in each
150 frame at random locations and with random orientiations of the
151 molecule. When :mdp:`nstlist` is larger than one,
152 :mdp:`nstlist` insertions are performed in a sphere with radius
153 :mdp:`rtpi` around a the same random location using the same
154 pair list. Since pair list construction is expensive,
155 one can perform several extra insertions with the same list
156 almost for free. The random seed is set with
157 :mdp:`ld-seed`. The temperature for the Boltzmann weighting is
158 set with :mdp:`ref-t`, this should match the temperature of the
159 simulation of the original trajectory. Dispersion correction is
160 implemented correctly for TPI. All relevant quantities are
161 written to the file specified with ``mdrun -tpi``. The
162 distribution of insertion energies is written to the file
163 specified with ``mdrun -tpid``. No trajectory or energy file is
164 written. Parallel TPI gives identical results to single-node
165 TPI. For charged molecules, using PME with a fine grid is most
166 accurate and also efficient, since the potential in the system
167 only needs to be calculated once per frame.
171 Test particle insertion into a predefined cavity location. The
172 procedure is the same as for :mdp-value:`integrator=tpi`, except
173 that one coordinate extra is read from the trajectory, which is
174 used as the insertion location. The molecule to be inserted
175 should be centered at 0,0,0. |Gromacs| does not do this for you,
176 since for different situations a different way of centering
177 might be optimal. Also :mdp:`rtpi` sets the radius for the
178 sphere around this location. Neighbor searching is done only
179 once per frame, :mdp:`nstlist` is not used. Parallel
180 :mdp-value:`integrator=tpic` gives identical results to
181 single-rank :mdp-value:`integrator=tpic`.
185 Enable MiMiC QM/MM coupling to run hybrid molecular dynamics.
186 Keey in mind that its required to launch CPMD compiled with MiMiC as well.
187 In this mode all options regarding integration (T-coupling, P-coupling,
188 timestep and number of steps) are ignored as CPMD will do the integration
189 instead. Options related to forces computation (cutoffs, PME parameters,
190 etc.) are working as usual. Atom selection to define QM atoms is read
191 from :mdp:`QMMM-grps`
196 starting time for your run (only makes sense for time-based
202 time step for integration (only makes sense for time-based
208 maximum number of steps to integrate or minimize, -1 is no
214 The starting step. The time at step i in a run is
215 calculated as: t = :mdp:`tinit` + :mdp:`dt` *
216 (:mdp:`init-step` + i). The free-energy lambda is calculated
217 as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
218 (:mdp:`init-step` + i). Also non-equilibrium MD parameters can
219 depend on the step number. Thus for exact restarts or redoing
220 part of a run it might be necessary to set :mdp:`init-step` to
221 the step number of the restart frame. :ref:`gmx convert-tpr`
222 does this automatically.
224 .. mdp:: simulation-part
227 A simulation can consist of multiple parts, each of which has
228 a part number. This option specifies what that number will
229 be, which helps keep track of parts that are logically the
230 same simulation. This option is generally useful to set only
231 when coping with a crashed simulation where files were lost.
235 .. mdp-value:: Linear
237 Remove center of mass translational velocity
239 .. mdp-value:: Angular
241 Remove center of mass translational and rotational velocity
243 .. mdp-value:: Linear-acceleration-correction
245 Remove center of mass translational velocity. Correct the center of
246 mass position assuming linear acceleration over :mdp:`nstcomm` steps.
247 This is useful for cases where an acceleration is expected on the
248 center of mass which is nearly constant over :mdp:`nstcomm` steps.
249 This can occur for example when pulling on a group using an absolute
254 No restriction on the center of mass motion
259 frequency for center of mass motion removal
263 group(s) for center of mass motion removal, default is the whole
272 (0) [amu ps\ :sup:`-1`]
273 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
274 the friction coefficient for each particle is calculated as mass/
280 used to initialize random generator for thermal noise for
281 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
282 a pseudo random seed is used. When running BD or SD on multiple
283 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
284 the processor number.
292 (10.0) [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
293 the minimization is converged when the maximum force is smaller
304 frequency of performing 1 steepest descent step while doing
305 conjugate gradient energy minimization.
310 Number of correction steps to use for L-BFGS minimization. A higher
311 number is (at least theoretically) more accurate, but slower.
314 Shell Molecular Dynamics
315 ^^^^^^^^^^^^^^^^^^^^^^^^
317 When shells or flexible constraints are present in the system the
318 positions of the shells and the lengths of the flexible constraints
319 are optimized at every time step until either the RMS force on the
320 shells and constraints is less than :mdp:`emtol`, or a maximum number
321 of iterations :mdp:`niter` has been reached. Minimization is converged
322 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
323 value should be 1.0 at most.
328 maximum number of iterations for optimizing the shell positions and
329 the flexible constraints.
334 the step size for optimizing the flexible constraints. Should be
335 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
336 particles in a flexible constraint and d2V/dq2 is the second
337 derivative of the potential in the constraint direction. Hopefully
338 this number does not differ too much between the flexible
339 constraints, as the number of iterations and thus the runtime is
340 very sensitive to fcstep. Try several values!
343 Test particle insertion
344 ^^^^^^^^^^^^^^^^^^^^^^^
349 the test particle insertion radius, see integrators
350 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
359 number of steps that elapse between writing coordinates to the output
360 trajectory file (:ref:`trr`), the last coordinates are always written
365 number of steps that elapse between writing velocities to the output
366 trajectory file (:ref:`trr`), the last velocities are always written
371 number of steps that elapse between writing forces to the output
372 trajectory file (:ref:`trr`), the last forces are always written.
377 number of steps that elapse between writing energies to the log
378 file, the last energies are always written
380 .. mdp:: nstcalcenergy
383 number of steps that elapse between calculating the energies, 0 is
384 never. This option is only relevant with dynamics. This option affects the
385 performance in parallel simulations, because calculating energies
386 requires global communication between all processes which can
387 become a bottleneck at high parallelization.
392 number of steps that elapse between writing energies to energy file,
393 the last energies are always written, should be a multiple of
394 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
395 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
396 energy file, so :ref:`gmx energy` can report exact energy averages
397 and fluctuations also when :mdp:`nstenergy` > 1
399 .. mdp:: nstxout-compressed
402 number of steps that elapse between writing position coordinates
403 using lossy compression (:ref:`xtc` file)
405 .. mdp:: compressed-x-precision
408 precision with which to write to the compressed trajectory file
410 .. mdp:: compressed-x-grps
412 group(s) to write to the compressed trajectory file, by default the
413 whole system is written (if :mdp:`nstxout-compressed` > 0)
417 group(s) for which to write to write short-ranged non-bonded
418 potential energies to the energy file (not supported on GPUs)
424 .. mdp:: cutoff-scheme
426 .. mdp-value:: Verlet
428 Generate a pair list with buffering. The buffer size is
429 automatically set based on :mdp:`verlet-buffer-tolerance`,
430 unless this is set to -1, in which case :mdp:`rlist` will be
431 used. This option has an explicit, exact cut-off at :mdp:`rvdw`
432 equal to :mdp:`rcoulomb`, unless PME or Ewald is used, in which
433 case :mdp:`rcoulomb` > :mdp:`rvdw` is allowed. Currently only
434 cut-off, reaction-field, PME or Ewald electrostatics and plain
435 LJ are supported. Some :ref:`gmx mdrun` functionality is not yet
436 supported with the :mdp-value:`cutoff-scheme=Verlet` scheme, but :ref:`gmx grompp`
437 checks for this. Native GPU acceleration is only supported with
438 :mdp-value:`cutoff-scheme=Verlet`. With GPU-accelerated PME or with separate PME
439 ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
440 balance by scaling :mdp:`rcoulomb` and the grid spacing. This
441 can be turned off with ``mdrun -notunepme``. :mdp-value:`cutoff-scheme=Verlet` is
442 faster than :mdp-value:`cutoff-scheme=group` when there is no water, or if
443 :mdp-value:`cutoff-scheme=group` would use a pair-list buffer to conserve energy.
447 Generate a pair list for groups of atoms. These groups
448 correspond to the charge groups in the topology. This was the
449 only cut-off treatment scheme before version 4.6, and is
450 **deprecated since 5.1**. There is no explicit buffering of
451 the pair list. This enables efficient force calculations for
452 water, but energy is only conserved when a buffer is explicitly
461 Frequency to update the neighbor list. When this is 0, the
462 neighbor list is made only once. With energy minimization the
463 pair list will be updated for every energy evaluation when
464 :mdp:`nstlist` is greater than 0. With :mdp-value:`cutoff-scheme=Verlet` and
465 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
466 a minimum value and :ref:`gmx mdrun` might increase it, unless
467 it is set to 1. With parallel simulations and/or non-bonded
468 force calculation on the GPU, a value of 20 or 40 often gives
469 the best performance. With :mdp-value:`cutoff-scheme=group` and non-exact
470 cut-off's, :mdp:`nstlist` will affect the accuracy of your
471 simulation and it can not be chosen freely.
475 The neighbor list is only constructed once and never
476 updated. This is mainly useful for vacuum simulations in which
477 all particles see each other.
487 Make a grid in the box and only check atoms in neighboring grid
488 cells when constructing a new neighbor list every
489 :mdp:`nstlist` steps. In large systems grid search is much
490 faster than simple search.
492 .. mdp-value:: simple
494 Check every atom in the box when constructing a new neighbor
495 list every :mdp:`nstlist` steps (only with :mdp-value:`cutoff-scheme=group`
502 Use periodic boundary conditions in all directions.
506 Use no periodic boundary conditions, ignore the box. To simulate
507 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
508 best performance without cut-offs on a single MPI rank, set
509 :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`.
513 Use periodic boundary conditions in x and y directions
514 only. This works only with :mdp-value:`ns-type=grid` and can be used
515 in combination with walls_. Without walls or with only one wall
516 the system size is infinite in the z direction. Therefore
517 pressure coupling or Ewald summation methods can not be
518 used. These disadvantages do not apply when two walls are used.
520 .. mdp:: periodic-molecules
524 molecules are finite, fast molecular PBC can be used
528 for systems with molecules that couple to themselves through the
529 periodic boundary conditions, this requires a slower PBC
530 algorithm and molecules are not made whole in the output
532 .. mdp:: verlet-buffer-tolerance
534 (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
536 Useful only with the :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`. This sets
537 the maximum allowed error for pair interactions per particle caused
538 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
539 :mdp:`nstlist` and the Verlet buffer size are fixed (for
540 performance reasons), particle pairs not in the pair list can
541 occasionally get within the cut-off distance during
542 :mdp:`nstlist` -1 steps. This causes very small jumps in the
543 energy. In a constant-temperature ensemble, these very small energy
544 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
545 estimate assumes a homogeneous particle distribution, hence the
546 errors might be slightly underestimated for multi-phase
547 systems. (See the `reference manual`_ for details). For longer
548 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
549 overestimated, because the interactions between particles are
550 ignored. Combined with cancellation of errors, the actual drift of
551 the total energy is usually one to two orders of magnitude
552 smaller. Note that the generated buffer size takes into account
553 that the |Gromacs| pair-list setup leads to a reduction in the
554 drift by a factor 10, compared to a simple particle-pair based
555 list. Without dynamics (energy minimization etc.), the buffer is 5%
556 of the cut-off. For NVE simulations the initial temperature is
557 used, unless this is zero, in which case a buffer of 10% is
558 used. For NVE simulations the tolerance usually needs to be lowered
559 to achieve proper energy conservation on the nanosecond time
560 scale. To override the automated buffer setting, use
561 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
566 Cut-off distance for the short-range neighbor list. With dynamics,
567 this is by default set by the :mdp:`verlet-buffer-tolerance` option
568 and the value of :mdp:`rlist` is ignored. Without dynamics, this
569 is by default set to the maximum cut-off plus 5% buffer, except
570 for test particle insertion, where the buffer is managed exactly
579 .. mdp-value:: Cut-off
581 Plain cut-off with pair list radius :mdp:`rlist` and
582 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
587 Classical Ewald sum electrostatics. The real-space cut-off
588 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
589 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
590 of wave vectors used in reciprocal space is controlled by
591 :mdp:`fourierspacing`. The relative accuracy of
592 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
594 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
595 large systems. It is included mainly for reference - in most
596 cases PME will perform much better.
600 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
601 space is similar to the Ewald sum, while the reciprocal part is
602 performed with FFTs. Grid dimensions are controlled with
603 :mdp:`fourierspacing` and the interpolation order with
604 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
605 interpolation the electrostatic forces have an accuracy of
606 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
607 this you might try 0.15 nm. When running in parallel the
608 interpolation parallelizes better than the FFT, so try
609 decreasing grid dimensions while increasing interpolation.
611 .. mdp-value:: P3M-AD
613 Particle-Particle Particle-Mesh algorithm with analytical
614 derivative for for long range electrostatic interactions. The
615 method and code is identical to SPME, except that the influence
616 function is optimized for the grid. This gives a slight increase
619 .. mdp-value:: Reaction-Field
621 Reaction field electrostatics with Coulomb cut-off
622 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
623 dielectric constant beyond the cut-off is
624 :mdp:`epsilon-rf`. The dielectric constant can be set to
625 infinity by setting :mdp:`epsilon-rf` =0.
627 .. mdp-value:: Reaction-Field-zero
629 In |Gromacs|, normal reaction-field electrostatics with
630 :mdp-value:`cutoff-scheme=group` leads to bad energy
631 conservation. :mdp-value:`coulombtype=Reaction-Field-zero` solves this by making
632 the potential zero beyond the cut-off. It can only be used with
633 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
634 only for that value the force vanishes at the
635 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
636 :mdp:`rcoulomb` to accommodate the size of charge groups
637 and diffusion between neighbor list updates. This, and the fact
638 that table lookups are used instead of analytical functions make
639 reaction-field-zero computationally more expensive than
640 normal reaction-field.
644 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
645 might want to use :mdp-value:`coulombtype=Reaction-Field-zero` instead, which has
646 a similar potential shape, but has a physical interpretation and
647 has better energies due to the exclusion correction terms.
649 .. mdp-value:: Encad-Shift
651 The Coulomb potential is decreased over the whole range, using
652 the definition from the Encad simulation package.
654 .. mdp-value:: Switch
656 Analogous to :mdp-value:`vdwtype=Switch` for
657 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
658 serious artifacts, advice: use :mdp-value:`coulombtype=Reaction-Field-zero`
663 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
664 with user-defined potential functions for repulsion, dispersion
665 and Coulomb. When pair interactions are present, :ref:`gmx
666 mdrun` also expects to find a file ``tablep.xvg`` for the pair
667 interactions. When the same interactions should be used for
668 non-bonded and pair interactions the user can specify the same
669 file name for both table files. These files should contain 7
670 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
671 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
672 function, ``g(x)`` the dispersion function and ``h(x)`` the
673 repulsion function. When :mdp:`vdwtype` is not set to User the
674 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
675 the non-bonded interactions ``x`` values should run from 0 to
676 the largest cut-off distance + :mdp:`table-extension` and
677 should be uniformly spaced. For the pair interactions the table
678 length in the file will be used. The optimal spacing, which is
679 used for non-user tables, is ``0.002 nm`` when you run in mixed
680 precision or ``0.0005 nm`` when you run in double precision. The
681 function value at ``x=0`` is not important. More information is
682 in the printed manual.
684 .. mdp-value:: PME-Switch
686 A combination of PME and a switch function for the direct-space
687 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
688 :mdp:`rlist`. This is mainly useful constant energy simulations
689 (note that using PME with :mdp-value:`cutoff-scheme=Verlet`
690 will be more efficient).
692 .. mdp-value:: PME-User
694 A combination of PME and user tables (see
695 above). :mdp:`rcoulomb` is allowed to be smaller than
696 :mdp:`rlist`. The PME mesh contribution is subtracted from the
697 user table by :ref:`gmx mdrun`. Because of this subtraction the
698 user tables should contain about 10 decimal places.
700 .. mdp-value:: PME-User-Switch
702 A combination of PME-User and a switching function (see
703 above). The switching function is applied to final
704 particle-particle interaction, *i.e.* both to the user supplied
705 function and the PME Mesh correction part.
707 .. mdp:: coulomb-modifier
709 .. mdp-value:: Potential-shift
711 Shift the Coulomb potential by a constant such that it is zero
712 at the cut-off. This makes the potential the integral of the
713 force. Note that this does not affect the forces or the
718 Use an unmodified Coulomb potential. This can be useful
719 when comparing energies with those computed with other software.
721 .. mdp:: rcoulomb-switch
724 where to start switching the Coulomb potential, only relevant
725 when force or potential switching is used
730 The distance for the Coulomb cut-off. Note that with PME this value
731 can be increased by the PME tuning in :ref:`gmx mdrun` along with
732 the PME grid spacing.
737 The relative dielectric constant. A value of 0 means infinity.
742 The relative dielectric constant of the reaction field. This
743 is only used with reaction-field electrostatics. A value of 0
752 .. mdp-value:: Cut-off
754 Plain cut-off with pair list radius :mdp:`rlist` and VdW
755 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
759 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
760 grid dimensions are controlled with :mdp:`fourierspacing` in
761 the same way as for electrostatics, and the interpolation order
762 is controlled with :mdp:`pme-order`. The relative accuracy of
763 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
764 and the specific combination rules that are to be used by the
765 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
769 This functionality is deprecated and replaced by using
770 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
771 The LJ (not Buckingham) potential is decreased over the whole range and
772 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
773 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
774 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
775 size of charge groups and diffusion between neighbor list
778 .. mdp-value:: Switch
780 This functionality is deprecated and replaced by using
781 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
782 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
783 which it is switched off to reach zero at :mdp:`rvdw`. Both the
784 potential and force functions are continuously smooth, but be
785 aware that all switch functions will give rise to a bulge
786 (increase) in the force (since we are switching the
787 potential). The neighbor search cut-off :mdp:`rlist` should be
788 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
789 size of charge groups and diffusion between neighbor list
792 .. mdp-value:: Encad-Shift
794 The LJ (not Buckingham) potential is decreased over the whole
795 range, using the definition from the Encad simulation package.
799 See user for :mdp:`coulombtype`. The function value at zero is
800 not important. When you want to use LJ correction, make sure
801 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
802 function. When :mdp:`coulombtype` is not set to User the values
803 for the ``f`` and ``-f'`` columns are ignored.
805 .. mdp:: vdw-modifier
807 .. mdp-value:: Potential-shift
809 Shift the Van der Waals potential by a constant such that it is
810 zero at the cut-off. This makes the potential the integral of
811 the force. Note that this does not affect the forces or the
816 Use an unmodified Van der Waals potential. This can be useful
817 when comparing energies with those computed with other software.
819 .. mdp-value:: Force-switch
821 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
822 and :mdp:`rvdw`. This shifts the potential shift over the whole
823 range and switches it to zero at the cut-off. Note that this is
824 more expensive to calculate than a plain cut-off and it is not
825 required for energy conservation, since Potential-shift
826 conserves energy just as well.
828 .. mdp-value:: Potential-switch
830 Smoothly switches the potential to zero between
831 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
832 articifically large forces in the switching region and is much
833 more expensive to calculate. This option should only be used if
834 the force field you are using requires this.
839 where to start switching the LJ force and possibly the potential,
840 only relevant when force or potential switching is used
845 distance for the LJ or Buckingham cut-off
851 don't apply any correction
853 .. mdp-value:: EnerPres
855 apply long range dispersion corrections for Energy and Pressure
859 apply long range dispersion corrections for Energy only
865 .. mdp:: table-extension
868 Extension of the non-bonded potential lookup tables beyond the
869 largest cut-off distance. The value should be large enough to
870 account for charge group sizes and the diffusion between
871 neighbor-list updates. Without user defined potential the same
872 table length is used for the lookup tables for the 1-4
873 interactions, which are always tabulated irrespective of the use of
874 tables for the non-bonded interactions. The value of
875 :mdp:`table-extension` in no way affects the values of
876 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
878 .. mdp:: energygrp-table
880 When user tables are used for electrostatics and/or VdW, here one
881 can give pairs of energy groups for which seperate user tables
882 should be used. The two energy groups will be appended to the table
883 file name, in order of their definition in :mdp:`energygrps`,
884 seperated by underscores. For example, if ``energygrps = Na Cl
885 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
886 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
887 normal ``table.xvg`` which will be used for all other energy group
894 .. mdp:: fourierspacing
897 For ordinary Ewald, the ratio of the box dimensions and the spacing
898 determines a lower bound for the number of wave vectors to use in
899 each (signed) direction. For PME and P3M, that ratio determines a
900 lower bound for the number of Fourier-space grid points that will
901 be used along that axis. In all cases, the number for each
902 direction can be overridden by entering a non-zero value for that
903 :mdp:`fourier-nx` direction. For optimizing the relative load of
904 the particle-particle interactions and the mesh part of PME, it is
905 useful to know that the accuracy of the electrostatics remains
906 nearly constant when the Coulomb cut-off and the PME grid spacing
907 are scaled by the same factor. Note that this spacing can be scaled
908 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
915 Highest magnitude of wave vectors in reciprocal space when using Ewald.
916 Grid size when using PME or P3M. These values override
917 :mdp:`fourierspacing` per direction. The best choice is powers of
918 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
919 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
925 Interpolation order for PME. 4 equals cubic interpolation. You
926 might try 6/8/10 when running in parallel and simultaneously
927 decrease grid dimension.
932 The relative strength of the Ewald-shifted direct potential at
933 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
934 will give a more accurate direct sum, but then you need more wave
935 vectors for the reciprocal sum.
937 .. mdp:: ewald-rtol-lj
940 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
941 to control the relative strength of the dispersion potential at
942 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
943 electrostatic potential.
945 .. mdp:: lj-pme-comb-rule
948 The combination rules used to combine VdW-parameters in the
949 reciprocal part of LJ-PME. Geometric rules are much faster than
950 Lorentz-Berthelot and usually the recommended choice, even when the
951 rest of the force field uses the Lorentz-Berthelot rules.
953 .. mdp-value:: Geometric
955 Apply geometric combination rules
957 .. mdp-value:: Lorentz-Berthelot
959 Apply Lorentz-Berthelot combination rules
961 .. mdp:: ewald-geometry
965 The Ewald sum is performed in all three dimensions.
969 The reciprocal sum is still performed in 3D, but a force and
970 potential correction applied in the `z` dimension to produce a
971 pseudo-2D summation. If your system has a slab geometry in the
972 `x-y` plane you can try to increase the `z`-dimension of the box
973 (a box height of 3 times the slab height is usually ok) and use
976 .. mdp:: epsilon-surface
979 This controls the dipole correction to the Ewald summation in
980 3D. The default value of zero means it is turned off. Turn it on by
981 setting it to the value of the relative permittivity of the
982 imaginary surface around your infinite system. Be careful - you
983 shouldn't use this if you have free mobile charges in your
984 system. This value does not affect the slab 3DC variant of the long
995 No temperature coupling.
997 .. mdp-value:: berendsen
999 Temperature coupling with a Berendsen thermostat to a bath with
1000 temperature :mdp:`ref-t`, with time constant
1001 :mdp:`tau-t`. Several groups can be coupled separately, these
1002 are specified in the :mdp:`tc-grps` field separated by spaces.
1004 .. mdp-value:: nose-hoover
1006 Temperature coupling using a Nose-Hoover extended ensemble. The
1007 reference temperature and coupling groups are selected as above,
1008 but in this case :mdp:`tau-t` controls the period of the
1009 temperature fluctuations at equilibrium, which is slightly
1010 different from a relaxation time. For NVT simulations the
1011 conserved energy quantity is written to the energy and log files.
1013 .. mdp-value:: andersen
1015 Temperature coupling by randomizing a fraction of the particle velocities
1016 at each timestep. Reference temperature and coupling groups are
1017 selected as above. :mdp:`tau-t` is the average time between
1018 randomization of each molecule. Inhibits particle dynamics
1019 somewhat, but little or no ergodicity issues. Currently only
1020 implemented with velocity Verlet, and not implemented with
1023 .. mdp-value:: andersen-massive
1025 Temperature coupling by randomizing velocities of all particles at
1026 infrequent timesteps. Reference temperature and coupling groups are
1027 selected as above. :mdp:`tau-t` is the time between
1028 randomization of all molecules. Inhibits particle dynamics
1029 somewhat, but little or no ergodicity issues. Currently only
1030 implemented with velocity Verlet.
1032 .. mdp-value:: v-rescale
1034 Temperature coupling using velocity rescaling with a stochastic
1035 term (JCP 126, 014101). This thermostat is similar to Berendsen
1036 coupling, with the same scaling using :mdp:`tau-t`, but the
1037 stochastic term ensures that a proper canonical ensemble is
1038 generated. The random seed is set with :mdp:`ld-seed`. This
1039 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1040 simulations the conserved energy quantity is written to the
1041 energy and log file.
1046 The frequency for coupling the temperature. The default value of -1
1047 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1048 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1049 Verlet integrators :mdp:`nsttcouple` is set to 1.
1051 .. mdp:: nh-chain-length
1054 The number of chained Nose-Hoover thermostats for velocity Verlet
1055 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1056 only supports 1. Data for the NH chain variables is not printed
1057 to the :ref:`edr` file by default, but can be turned on with the
1058 :mdp:`print-nose-hoover-chain-variables` option.
1060 .. mdp:: print-nose-hoover-chain-variables
1064 Do not store Nose-Hoover chain variables in the energy file.
1068 Store all positions and velocities of the Nose-Hoover chain
1073 groups to couple to separate temperature baths
1078 time constant for coupling (one for each group in
1079 :mdp:`tc-grps`), -1 means no temperature coupling
1084 reference temperature for coupling (one for each group in
1095 No pressure coupling. This means a fixed box size.
1097 .. mdp-value:: Berendsen
1099 Exponential relaxation pressure coupling with time constant
1100 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1101 argued that this does not yield a correct thermodynamic
1102 ensemble, but it is the most efficient way to scale a box at the
1105 .. mdp-value:: Parrinello-Rahman
1107 Extended-ensemble pressure coupling where the box vectors are
1108 subject to an equation of motion. The equation of motion for the
1109 atoms is coupled to this. No instantaneous scaling takes
1110 place. As for Nose-Hoover temperature coupling the time constant
1111 :mdp:`tau-p` is the period of pressure fluctuations at
1112 equilibrium. This is probably a better method when you want to
1113 apply pressure scaling during data collection, but beware that
1114 you can get very large oscillations if you are starting from a
1115 different pressure. For simulations where the exact fluctations
1116 of the NPT ensemble are important, or if the pressure coupling
1117 time is very short it may not be appropriate, as the previous
1118 time step pressure is used in some steps of the |Gromacs|
1119 implementation for the current time step pressure.
1123 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1124 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1125 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1126 time constant :mdp:`tau-p` is the period of pressure
1127 fluctuations at equilibrium. This is probably a better method
1128 when you want to apply pressure scaling during data collection,
1129 but beware that you can get very large oscillations if you are
1130 starting from a different pressure. Currently (as of version
1131 5.1), it only supports isotropic scaling, and only works without
1136 Specifies the kind of isotropy of the pressure coupling used. Each
1137 kind takes one or more values for :mdp:`compressibility` and
1138 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1140 .. mdp-value:: isotropic
1142 Isotropic pressure coupling with time constant
1143 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1144 :mdp:`ref-p` is required.
1146 .. mdp-value:: semiisotropic
1148 Pressure coupling which is isotropic in the ``x`` and ``y``
1149 direction, but different in the ``z`` direction. This can be
1150 useful for membrane simulations. Two values each for
1151 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1152 ``x/y`` and ``z`` directions respectively.
1154 .. mdp-value:: anisotropic
1156 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1157 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1158 respectively. When the off-diagonal compressibilities are set to
1159 zero, a rectangular box will stay rectangular. Beware that
1160 anisotropic scaling can lead to extreme deformation of the
1163 .. mdp-value:: surface-tension
1165 Surface tension coupling for surfaces parallel to the
1166 xy-plane. Uses normal pressure coupling for the `z`-direction,
1167 while the surface tension is coupled to the `x/y` dimensions of
1168 the box. The first :mdp:`ref-p` value is the reference surface
1169 tension times the number of surfaces ``bar nm``, the second
1170 value is the reference `z`-pressure ``bar``. The two
1171 :mdp:`compressibility` values are the compressibility in the
1172 `x/y` and `z` direction respectively. The value for the
1173 `z`-compressibility should be reasonably accurate since it
1174 influences the convergence of the surface-tension, it can also
1175 be set to zero to have a box with constant height.
1180 The frequency for coupling the pressure. The default value of -1
1181 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1182 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1183 Verlet integrators :mdp:`nstpcouple` is set to 1.
1188 The time constant for pressure coupling (one value for all
1191 .. mdp:: compressibility
1194 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1195 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1196 required values is implied by :mdp:`pcoupltype`.
1201 The reference pressure for coupling. The number of required values
1202 is implied by :mdp:`pcoupltype`.
1204 .. mdp:: refcoord-scaling
1208 The reference coordinates for position restraints are not
1209 modified. Note that with this option the virial and pressure
1210 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1215 The reference coordinates are scaled with the scaling matrix of
1216 the pressure coupling.
1220 Scale the center of mass of the reference coordinates with the
1221 scaling matrix of the pressure coupling. The vectors of each
1222 reference coordinate to the center of mass are not scaled. Only
1223 one COM is used, even when there are multiple molecules with
1224 position restraints. For calculating the COM of the reference
1225 coordinates in the starting configuration, periodic boundary
1226 conditions are not taken into account. Note that with this option
1227 the virial and pressure might be ill defined, see
1228 :ref:`here <reference-manual-position-restraints>` for more details.
1234 Simulated annealing is controlled separately for each temperature
1235 group in |Gromacs|. The reference temperature is a piecewise linear
1236 function, but you can use an arbitrary number of points for each
1237 group, and choose either a single sequence or a periodic behaviour for
1238 each group. The actual annealing is performed by dynamically changing
1239 the reference temperature used in the thermostat algorithm selected,
1240 so remember that the system will usually not instantaneously reach the
1241 reference temperature!
1245 Type of annealing for each temperature group
1249 No simulated annealing - just couple to reference temperature value.
1251 .. mdp-value:: single
1253 A single sequence of annealing points. If your simulation is
1254 longer than the time of the last point, the temperature will be
1255 coupled to this constant value after the annealing sequence has
1256 reached the last time point.
1258 .. mdp-value:: periodic
1260 The annealing will start over at the first reference point once
1261 the last reference time is reached. This is repeated until the
1264 .. mdp:: annealing-npoints
1266 A list with the number of annealing reference/control points used
1267 for each temperature group. Use 0 for groups that are not
1268 annealed. The number of entries should equal the number of
1271 .. mdp:: annealing-time
1273 List of times at the annealing reference/control points for each
1274 group. If you are using periodic annealing, the times will be used
1275 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1276 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1277 etc. The number of entries should equal the sum of the numbers
1278 given in :mdp:`annealing-npoints`.
1280 .. mdp:: annealing-temp
1282 List of temperatures at the annealing reference/control points for
1283 each group. The number of entries should equal the sum of the
1284 numbers given in :mdp:`annealing-npoints`.
1286 Confused? OK, let's use an example. Assume you have two temperature
1287 groups, set the group selections to ``annealing = single periodic``,
1288 the number of points of each group to ``annealing-npoints = 3 4``, the
1289 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1290 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1291 will be coupled to 298K at 0ps, but the reference temperature will
1292 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1293 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1294 second group is coupled to 298K at 0ps, it increases linearly to 320K
1295 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1296 decreases to 298K, and then it starts over with the same pattern
1297 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1298 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1308 Do not generate velocities. The velocities are set to zero
1309 when there are no velocities in the input structure file.
1313 Generate velocities in :ref:`gmx grompp` according to a
1314 Maxwell distribution at temperature :mdp:`gen-temp`, with
1315 random seed :mdp:`gen-seed`. This is only meaningful with
1316 :mdp-value:`integrator=md`.
1321 temperature for Maxwell distribution
1326 used to initialize random generator for random velocities,
1327 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1334 .. mdp:: constraints
1336 Controls which bonds in the topology will be converted to rigid
1337 holonomic constraints. Note that typical rigid water models do not
1338 have bonds, but rather a specialized ``[settles]`` directive, so
1339 are not affected by this keyword.
1343 No bonds converted to constraints.
1345 .. mdp-value:: h-bonds
1347 Convert the bonds with H-atoms to constraints.
1349 .. mdp-value:: all-bonds
1351 Convert all bonds to constraints.
1353 .. mdp-value:: h-angles
1355 Convert all bonds to constraints and convert the angles that
1356 involve H-atoms to bond-constraints.
1358 .. mdp-value:: all-angles
1360 Convert all bonds to constraints and all angles to bond-constraints.
1362 .. mdp:: constraint-algorithm
1364 Chooses which solver satisfies any non-SETTLE holonomic
1367 .. mdp-value:: LINCS
1369 LINear Constraint Solver. With domain decomposition the parallel
1370 version P-LINCS is used. The accuracy in set with
1371 :mdp:`lincs-order`, which sets the number of matrices in the
1372 expansion for the matrix inversion. After the matrix inversion
1373 correction the algorithm does an iterative correction to
1374 compensate for lengthening due to rotation. The number of such
1375 iterations can be controlled with :mdp:`lincs-iter`. The root
1376 mean square relative constraint deviation is printed to the log
1377 file every :mdp:`nstlog` steps. If a bond rotates more than
1378 :mdp:`lincs-warnangle` in one step, a warning will be printed
1379 both to the log file and to ``stderr``. LINCS should not be used
1380 with coupled angle constraints.
1382 .. mdp-value:: SHAKE
1384 SHAKE is slightly slower and less stable than LINCS, but does
1385 work with angle constraints. The relative tolerance is set with
1386 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1387 does not support constraints between atoms on different nodes,
1388 thus it can not be used with domain decompositon when inter
1389 charge-group constraints are present. SHAKE can not be used with
1390 energy minimization.
1392 .. mdp:: continuation
1394 This option was formerly known as ``unconstrained-start``.
1398 apply constraints to the start configuration and reset shells
1402 do not apply constraints to the start configuration and do not
1403 reset shells, useful for exact coninuation and reruns
1408 relative tolerance for SHAKE
1410 .. mdp:: lincs-order
1413 Highest order in the expansion of the constraint coupling
1414 matrix. When constraints form triangles, an additional expansion of
1415 the same order is applied on top of the normal expansion only for
1416 the couplings within such triangles. For "normal" MD simulations an
1417 order of 4 usually suffices, 6 is needed for large time-steps with
1418 virtual sites or BD. For accurate energy minimization an order of 8
1419 or more might be required. With domain decomposition, the cell size
1420 is limited by the distance spanned by :mdp:`lincs-order` +1
1421 constraints. When one wants to scale further than this limit, one
1422 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1423 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1424 )* :mdp:`lincs-order` remains constant.
1429 Number of iterations to correct for rotational lengthening in
1430 LINCS. For normal runs a single step is sufficient, but for NVE
1431 runs where you want to conserve energy accurately or for accurate
1432 energy minimization you might want to increase it to 2.
1434 .. mdp:: lincs-warnangle
1437 maximum angle that a bond can rotate before LINCS will complain
1443 bonds are represented by a harmonic potential
1447 bonds are represented by a Morse potential
1450 Energy group exclusions
1451 ^^^^^^^^^^^^^^^^^^^^^^^
1453 .. mdp:: energygrp-excl
1455 Pairs of energy groups for which all non-bonded interactions are
1456 excluded. An example: if you have two energy groups ``Protein`` and
1457 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1458 would give only the non-bonded interactions between the protein and
1459 the solvent. This is especially useful for speeding up energy
1460 calculations with ``mdrun -rerun`` and for excluding interactions
1461 within frozen groups.
1470 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1471 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1472 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1473 used (it is usually best to use semiisotropic pressure coupling
1474 with the ``x/y`` compressibility set to 0, as otherwise the surface
1475 area will change). Walls interact wit the rest of the system
1476 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1477 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1478 monitor the interaction of energy groups with each wall. The center
1479 of mass motion removal will be turned off in the ``z``-direction.
1481 .. mdp:: wall-atomtype
1483 the atom type name in the force field for each wall. By (for
1484 example) defining a special wall atom type in the topology with its
1485 own combination rules, this allows for independent tuning of the
1486 interaction of each atomtype with the walls.
1492 LJ integrated over the volume behind the wall: 9-3 potential
1496 LJ integrated over the wall surface: 10-4 potential
1500 direct LJ potential with the ``z`` distance from the wall
1504 user defined potentials indexed with the ``z`` distance from the
1505 wall, the tables are read analogously to the
1506 :mdp:`energygrp-table` option, where the first name is for a
1507 "normal" energy group and the second name is ``wall0`` or
1508 ``wall1``, only the dispersion and repulsion columns are used
1510 .. mdp:: wall-r-linpot
1513 Below this distance from the wall the potential is continued
1514 linearly and thus the force is constant. Setting this option to a
1515 postive value is especially useful for equilibration when some
1516 atoms are beyond a wall. When the value is <=0 (<0 for
1517 :mdp:`wall-type` =table), a fatal error is generated when atoms
1520 .. mdp:: wall-density
1522 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1523 the number density of the atoms for each wall for wall types 9-3
1526 .. mdp:: wall-ewald-zfac
1529 The scaling factor for the third box vector for Ewald summation
1530 only, the minimum is 2. Ewald summation can only be used with
1531 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1532 ``=3dc``. The empty layer in the box serves to decrease the
1533 unphysical Coulomb interaction between periodic images.
1539 Note that where pulling coordinates are applicable, there can be more
1540 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1541 variables will exist accordingly. Documentation references to things
1542 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1543 applicable pulling coordinate, eg. the second pull coordinate is described by
1544 pull-coord2-vec, pull-coord2-k, and so on.
1550 No center of mass pulling. All the following pull options will
1551 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1556 Center of mass pulling will be applied on 1 or more groups using
1557 1 or more pull coordinates.
1559 .. mdp:: pull-cylinder-r
1562 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1564 .. mdp:: pull-constr-tol
1567 the relative constraint tolerance for constraint pulling
1569 .. mdp:: pull-print-com
1573 do not print the COM for any group
1577 print the COM of all groups for all pull coordinates
1579 .. mdp:: pull-print-ref-value
1583 do not print the reference value for each pull coordinate
1587 print the reference value for each pull coordinate
1589 .. mdp:: pull-print-components
1593 only print the distance for each pull coordinate
1597 print the distance and Cartesian components selected in
1598 :mdp:`pull-coord1-dim`
1600 .. mdp:: pull-nstxout
1603 frequency for writing out the COMs of all the pull group (0 is
1606 .. mdp:: pull-nstfout
1609 frequency for writing out the force of all the pulled group
1612 .. mdp:: pull-pbc-ref-prev-step-com
1616 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1617 treatment of periodic boundary conditions.
1621 Use the COM of the previous step as reference for the treatment
1622 of periodic boundary conditions. The reference is initialized
1623 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1624 be located centrally in the group. Using the COM from the
1625 previous step can be useful if one or more pull groups are large.
1627 .. mdp:: pull-xout-average
1631 Write the instantaneous coordinates for all the pulled groups.
1635 Write the average coordinates (since last output) for all the
1636 pulled groups. N.b., some analysis tools might expect instantaneous
1639 .. mdp:: pull-fout-average
1643 Write the instantaneous force for all the pulled groups.
1647 Write the average force (since last output) for all the
1648 pulled groups. N.b., some analysis tools might expect instantaneous
1651 .. mdp:: pull-ngroups
1654 The number of pull groups, not including the absolute reference
1655 group, when used. Pull groups can be reused in multiple pull
1656 coordinates. Below only the pull options for group 1 are given,
1657 further groups simply increase the group index number.
1659 .. mdp:: pull-ncoords
1662 The number of pull coordinates. Below only the pull options for
1663 coordinate 1 are given, further coordinates simply increase the
1664 coordinate index number.
1666 .. mdp:: pull-group1-name
1668 The name of the pull group, is looked up in the index file or in
1669 the default groups to obtain the atoms involved.
1671 .. mdp:: pull-group1-weights
1673 Optional relative weights which are multiplied with the masses of
1674 the atoms to give the total weight for the COM. The number should
1675 be 0, meaning all 1, or the number of atoms in the pull group.
1677 .. mdp:: pull-group1-pbcatom
1680 The reference atom for the treatment of periodic boundary
1681 conditions inside the group (this has no effect on the treatment of
1682 the pbc between groups). This option is only important when the
1683 diameter of the pull group is larger than half the shortest box
1684 vector. For determining the COM, all atoms in the group are put at
1685 their periodic image which is closest to
1686 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1687 atom (number wise) is used, which is only safe for small groups.
1688 :ref:`gmx grompp` checks that the maximum distance from the reference
1689 atom (specifically chosen, or not) to the other atoms in the group
1690 is not too large. This parameter is not used with
1691 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1692 weighting, which is useful for a group of molecules in a periodic
1693 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1696 .. mdp:: pull-coord1-type
1698 .. mdp-value:: umbrella
1700 Center of mass pulling using an umbrella potential between the
1701 reference group and one or more groups.
1703 .. mdp-value:: constraint
1705 Center of mass pulling using a constraint between the reference
1706 group and one or more groups. The setup is identical to the
1707 option umbrella, except for the fact that a rigid constraint is
1708 applied instead of a harmonic potential.
1710 .. mdp-value:: constant-force
1712 Center of mass pulling using a linear potential and therefore a
1713 constant force. For this option there is no reference position
1714 and therefore the parameters :mdp:`pull-coord1-init` and
1715 :mdp:`pull-coord1-rate` are not used.
1717 .. mdp-value:: flat-bottom
1719 At distances above :mdp:`pull-coord1-init` a harmonic potential
1720 is applied, otherwise no potential is applied.
1722 .. mdp-value:: flat-bottom-high
1724 At distances below :mdp:`pull-coord1-init` a harmonic potential
1725 is applied, otherwise no potential is applied.
1727 .. mdp-value:: external-potential
1729 An external potential that needs to be provided by another
1732 .. mdp:: pull-coord1-potential-provider
1734 The name of the external module that provides the potential for
1735 the case where :mdp:`pull-coord1-type` is external-potential.
1737 .. mdp:: pull-coord1-geometry
1739 .. mdp-value:: distance
1741 Pull along the vector connecting the two groups. Components can
1742 be selected with :mdp:`pull-coord1-dim`.
1744 .. mdp-value:: direction
1746 Pull in the direction of :mdp:`pull-coord1-vec`.
1748 .. mdp-value:: direction-periodic
1750 As :mdp-value:`pull-coord1-geometry=direction`, but allows the distance to be larger
1751 than half the box size. With this geometry the box should not be
1752 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1753 the pull force is not added to virial.
1755 .. mdp-value:: direction-relative
1757 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1758 that points from the COM of a third to the COM of a fourth pull
1759 group. This means that 4 groups need to be supplied in
1760 :mdp:`pull-coord1-groups`. Note that the pull force will give
1761 rise to a torque on the pull vector, which is turn leads to
1762 forces perpendicular to the pull vector on the two groups
1763 defining the vector. If you want a pull group to move between
1764 the two groups defining the vector, simply use the union of
1765 these two groups as the reference group.
1767 .. mdp-value:: cylinder
1769 Designed for pulling with respect to a layer where the reference
1770 COM is given by a local cylindrical part of the reference group.
1771 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1772 the first of the two groups in :mdp:`pull-coord1-groups` a
1773 cylinder is selected around the axis going through the COM of
1774 the second group with direction :mdp:`pull-coord1-vec` with
1775 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1776 continously to zero as the radial distance goes from 0 to
1777 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1778 dependence gives rise to radial forces on both pull groups.
1779 Note that the radius should be smaller than half the box size.
1780 For tilted cylinders they should be even smaller than half the
1781 box size since the distance of an atom in the reference group
1782 from the COM of the pull group has both a radial and an axial
1783 component. This geometry is not supported with constraint
1786 .. mdp-value:: angle
1788 Pull along an angle defined by four groups. The angle is
1789 defined as the angle between two vectors: the vector connecting
1790 the COM of the first group to the COM of the second group and
1791 the vector connecting the COM of the third group to the COM of
1794 .. mdp-value:: angle-axis
1796 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1797 Thus, only the two groups that define the first vector need to be given.
1799 .. mdp-value:: dihedral
1801 Pull along a dihedral angle defined by six groups. These pairwise
1802 define three vectors: the vector connecting the COM of group 1
1803 to the COM of group 2, the COM of group 3 to the COM of group 4,
1804 and the COM of group 5 to the COM group 6. The dihedral angle is
1805 then defined as the angle between two planes: the plane spanned by the
1806 the two first vectors and the plane spanned the two last vectors.
1809 .. mdp:: pull-coord1-groups
1811 The group indices on which this pull coordinate will operate.
1812 The number of group indices required is geometry dependent.
1813 The first index can be 0, in which case an
1814 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1815 absolute reference the system is no longer translation invariant
1816 and one should think about what to do with the center of mass
1819 .. mdp:: pull-coord1-dim
1822 Selects the dimensions that this pull coordinate acts on and that
1823 are printed to the output files when
1824 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1825 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1826 components set to Y contribute to the distance. Thus setting this
1827 to Y Y N results in a distance in the x/y plane. With other
1828 geometries all dimensions with non-zero entries in
1829 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1830 dimensions only affect the output.
1832 .. mdp:: pull-coord1-origin
1835 The pull reference position for use with an absolute reference.
1837 .. mdp:: pull-coord1-vec
1840 The pull direction. :ref:`gmx grompp` normalizes the vector.
1842 .. mdp:: pull-coord1-start
1846 do not modify :mdp:`pull-coord1-init`
1850 add the COM distance of the starting conformation to
1851 :mdp:`pull-coord1-init`
1853 .. mdp:: pull-coord1-init
1856 The reference distance or reference angle at t=0.
1858 .. mdp:: pull-coord1-rate
1860 (0) [nm/ps] or [deg/ps]
1861 The rate of change of the reference position or reference angle.
1863 .. mdp:: pull-coord1-k
1865 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1866 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1867 The force constant. For umbrella pulling this is the harmonic force
1868 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1869 for angles). For constant force pulling this is the
1870 force constant of the linear potential, and thus the negative (!)
1871 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1872 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1873 Note that for angles the force constant is expressed in terms of radians
1874 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1876 .. mdp:: pull-coord1-kB
1878 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1879 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1880 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1881 :mdp:`free-energy` is turned on. The force constant is then (1 -
1882 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1884 AWH adaptive biasing
1885 ^^^^^^^^^^^^^^^^^^^^
1895 Adaptively bias a reaction coordinate using the AWH method and estimate
1896 the corresponding PMF. The PMF and other AWH data are written to energy
1897 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1898 the ``gmx awh`` tool. The AWH coordinate can be
1899 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1900 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1901 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1902 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1904 .. mdp:: awh-potential
1906 .. mdp-value:: convolved
1908 The applied biasing potential is the convolution of the bias function and a
1909 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1910 in a smooth potential function and force. The resolution of the potential is set
1911 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1913 .. mdp-value:: umbrella
1915 The potential bias is applied by controlling the position of an harmonic potential
1916 using Monte-Carlo sampling. The force constant is set with
1917 :mdp:`awh1-dim1-force-constant`. The umbrella location
1918 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1919 There are no advantages to using an umbrella.
1920 This option is mainly for comparison and testing purposes.
1922 .. mdp:: awh-share-multisim
1926 AWH will not share biases across simulations started with
1927 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1931 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1932 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1933 with the biases with the same :mdp:`awh1-share-group` value.
1934 The simulations should have the same AWH settings for sharing to make sense.
1935 :ref:`gmx mdrun` will check whether the simulations are technically
1936 compatible for sharing, but the user should check that bias sharing
1937 physically makes sense.
1941 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1942 where -1 indicates to generate a seed. Only used with
1943 :mdp-value:`awh-potential=umbrella`.
1948 Number of steps between printing AWH data to the energy file, should be
1949 a multiple of :mdp:`nstenergy`.
1951 .. mdp:: awh-nstsample
1954 Number of steps between sampling of the coordinate value. This sampling
1955 is the basis for updating the bias and estimating the PMF and other AWH observables.
1957 .. mdp:: awh-nsamples-update
1960 The number of coordinate samples used for each AWH update.
1961 The update interval in steps is :mdp:`awh-nstsample` times this value.
1966 The number of biases, each acting on its own coordinate.
1967 The following options should be specified
1968 for each bias although below only the options for bias number 1 is shown. Options for
1969 other bias indices are obtained by replacing '1' by the bias index.
1971 .. mdp:: awh1-error-init
1973 (10.0) [kJ mol\ :sup:`-1`]
1974 Estimated initial average error of the PMF for this bias. This value together with the
1975 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1976 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1978 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1979 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1980 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1981 then :mdp:`awh1-error-init` should reflect that knowledge.
1983 .. mdp:: awh1-growth
1985 .. mdp-value:: exp-linear
1987 Each bias keeps a reference weight histogram for the coordinate samples.
1988 Its size sets the magnitude of the bias function and free energy estimate updates
1989 (few samples corresponds to large updates and vice versa).
1990 Thus, its growth rate sets the maximum convergence rate.
1991 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1992 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1993 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1994 high free energy barriers have not yet been flattened by the bias.
1996 .. mdp-value:: linear
1998 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1999 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
2000 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
2002 .. mdp:: awh1-equilibrate-histogram
2006 Do not equilibrate histogram.
2010 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
2011 histogram of sampled weights is following the target distribution closely enough (specifically,
2012 at least 80% of the target region needs to have a local relative error of less than 20%). This
2013 option would typically only be used when :mdp:`awh1-share-group` > 0
2014 and the initial configurations poorly represent the target
2017 .. mdp:: awh1-target
2019 .. mdp-value:: constant
2021 The bias is tuned towards a constant (uniform) coordinate distribution
2022 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
2024 .. mdp-value:: cutoff
2026 Similar to :mdp-value:`awh1-target=constant`, but the target
2027 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
2028 where F is the free energy relative to the estimated global minimum.
2029 This provides a smooth switch of a flat target distribution in
2030 regions with free energy lower than the cut-off to a Boltzmann
2031 distribution in regions with free energy higher than the cut-off.
2033 .. mdp-value:: boltzmann
2035 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
2036 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
2037 would give the same coordinate distribution as sampling with a simulation temperature
2040 .. mdp-value:: local-boltzmann
2042 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
2043 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
2044 change of the bias only depends on the local sampling. This local convergence property is
2045 only compatible with :mdp-value:`awh1-growth=linear`, since for
2046 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
2048 .. mdp:: awh1-target-beta-scaling
2051 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
2052 it is the unitless beta scaling factor taking values in (0,1).
2054 .. mdp:: awh1-target-cutoff
2056 (0) [kJ mol\ :sup:`-1`]
2057 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2059 .. mdp:: awh1-user-data
2063 Initialize the PMF and target distribution with default values.
2067 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2068 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2069 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2070 The file name can be changed with the ``-awh`` option.
2071 The first :mdp:`awh1-ndim` columns of
2072 each input file should contain the coordinate values, such that each row defines a point in
2073 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
2074 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2075 be in the same column as written by :ref:`gmx awh`.
2077 .. mdp:: awh1-share-group
2081 Do not share the bias.
2083 .. mdp-value:: positive
2085 Share the bias and PMF estimates within and/or between simulations.
2086 Within a simulation, the bias will be shared between biases that have the
2087 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2088 With :mdp-value:`awh-share-multisim=yes` and
2089 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2090 Sharing may increase convergence initially, although the starting configurations
2091 can be critical, especially when sharing between many biases.
2092 Currently, positive group values should start at 1 and increase
2093 by 1 for each subsequent bias that is shared.
2098 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2099 The following options should be specified for each such dimension. Below only
2100 the options for dimension number 1 is shown. Options for other dimension indices are
2101 obtained by replacing '1' by the dimension index.
2103 .. mdp:: awh1-dim1-coord-provider
2107 The module providing the reaction coordinate for this dimension.
2108 Currently AWH can only act on pull coordinates.
2110 .. mdp:: awh1-dim1-coord-index
2113 Index of the pull coordinate defining this coordinate dimension.
2115 .. mdp:: awh1-dim1-force-constant
2117 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2118 Force constant for the (convolved) umbrella potential(s) along this
2119 coordinate dimension.
2121 .. mdp:: awh1-dim1-start
2124 Start value of the sampling interval along this dimension. The range of allowed
2125 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2126 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2127 is allowed. The interval will then wrap around from +period/2 to -period/2.
2128 For the direction geometry, the dimension is made periodic when
2129 the direction is along a box vector and covers more than 95%
2130 of the box length. Note that one should not apply pressure coupling
2131 along a periodic dimension.
2133 .. mdp:: awh1-dim1-end
2136 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2138 .. mdp:: awh1-dim1-diffusion
2140 (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps]
2141 Estimated diffusion constant for this coordinate dimension determining the initial
2142 biasing rate. This needs only be a rough estimate and should not critically
2143 affect the results unless it is set to something very low, leading to slow convergence,
2144 or very high, forcing the system far from equilibrium. Not setting this value
2145 explicitly generates a warning.
2147 .. mdp:: awh1-dim1-cover-diameter
2150 Diameter that needs to be sampled by a single simulation around a coordinate value
2151 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2152 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2153 across each coordinate value.
2154 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2155 (:mdp:`awh1-share-group`>0).
2156 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2157 for many sharing simulations does not guarantee transitions across free energy barriers.
2158 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2159 has independently sampled the whole interval.
2164 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2165 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2166 that can be used to achieve such a rotation.
2172 No enforced rotation will be applied. All enforced rotation options will
2173 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2178 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2179 under the :mdp:`rot-group0` option.
2181 .. mdp:: rot-ngroups
2184 Number of rotation groups.
2188 Name of rotation group 0 in the index file.
2193 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2194 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2195 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2200 Use mass weighted rotation group positions.
2205 Rotation vector, will get normalized.
2210 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2214 (0) [degree ps\ :sup:`-1`]
2215 Reference rotation rate of group 0.
2219 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2220 Force constant for group 0.
2222 .. mdp:: rot-slab-dist0
2225 Slab distance, if a flexible axis rotation type was chosen.
2227 .. mdp:: rot-min-gauss0
2230 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2231 (for the flexible axis potentials).
2235 (0.0001) [nm\ :sup:`2`]
2236 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2238 .. mdp:: rot-fit-method0
2241 Fitting method when determining the actual angle of a rotation group
2242 (can be one of ``rmsd``, ``norm``, or ``potential``).
2244 .. mdp:: rot-potfit-nsteps0
2247 For fit type ``potential``, the number of angular positions around the reference angle for which the
2248 rotation potential is evaluated.
2250 .. mdp:: rot-potfit-step0
2253 For fit type ``potential``, the distance in degrees between two angular positions.
2255 .. mdp:: rot-nstrout
2258 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2259 and the rotation potential energy.
2261 .. mdp:: rot-nstsout
2264 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2274 ignore distance restraint information in topology file
2276 .. mdp-value:: simple
2278 simple (per-molecule) distance restraints.
2280 .. mdp-value:: ensemble
2282 distance restraints over an ensemble of molecules in one
2283 simulation box. Normally, one would perform ensemble averaging
2284 over multiple simulations, using ``mdrun
2285 -multidir``. The environment
2286 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2287 within each ensemble (usually equal to the number of directories
2288 supplied to ``mdrun -multidir``).
2290 .. mdp:: disre-weighting
2292 .. mdp-value:: equal
2294 divide the restraint force equally over all atom pairs in the
2297 .. mdp-value:: conservative
2299 the forces are the derivative of the restraint potential, this
2300 results in an weighting of the atom pairs to the reciprocal
2301 seventh power of the displacement. The forces are conservative
2302 when :mdp:`disre-tau` is zero.
2304 .. mdp:: disre-mixed
2308 the violation used in the calculation of the restraint force is
2309 the time-averaged violation
2313 the violation used in the calculation of the restraint force is
2314 the square root of the product of the time-averaged violation
2315 and the instantaneous violation
2319 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2320 force constant for distance restraints, which is multiplied by a
2321 (possibly) different factor for each restraint given in the `fac`
2322 column of the interaction in the topology file.
2327 time constant for distance restraints running average. A value of
2328 zero turns off time averaging.
2330 .. mdp:: nstdisreout
2333 period between steps when the running time-averaged and
2334 instantaneous distances of all atom pairs involved in restraints
2335 are written to the energy file (can make the energy file very
2342 ignore orientation restraint information in topology file
2346 use orientation restraints, ensemble averaging can be performed
2347 with ``mdrun -multidir``
2351 (0) [kJ mol\ :sup:`-1`]
2352 force constant for orientation restraints, which is multiplied by a
2353 (possibly) different weight factor for each restraint, can be set
2354 to zero to obtain the orientations from a free simulation
2359 time constant for orientation restraints running average. A value
2360 of zero turns off time averaging.
2362 .. mdp:: orire-fitgrp
2364 fit group for orientation restraining. This group of atoms is used
2365 to determine the rotation **R** of the system with respect to the
2366 reference orientation. The reference orientation is the starting
2367 conformation of the first subsystem. For a protein, backbone is a
2370 .. mdp:: nstorireout
2373 period between steps when the running time-averaged and
2374 instantaneous orientations for all restraints, and the molecular
2375 order tensor are written to the energy file (can make the energy
2379 Free energy calculations
2380 ^^^^^^^^^^^^^^^^^^^^^^^^
2382 .. mdp:: free-energy
2386 Only use topology A.
2390 Interpolate between topology A (lambda=0) to topology B
2391 (lambda=1) and write the derivative of the Hamiltonian with
2392 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2393 or the Hamiltonian differences with respect to other lambda
2394 values (as specified with foreign lambda) to the energy file
2395 and/or to ``dhdl.xvg``, where they can be processed by, for
2396 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2397 are interpolated linearly as described in the manual. When
2398 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2399 used for the LJ and Coulomb interactions.
2403 Turns on expanded ensemble simulation, where the alchemical state
2404 becomes a dynamic variable, allowing jumping between different
2405 Hamiltonians. See the expanded ensemble options for controlling how
2406 expanded ensemble simulations are performed. The different
2407 Hamiltonians used in expanded ensemble simulations are defined by
2408 the other free energy options.
2410 .. mdp:: init-lambda
2413 starting value for lambda (float). Generally, this should only be
2414 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2415 other cases, :mdp:`init-lambda-state` should be specified
2416 instead. Must be greater than or equal to 0.
2418 .. mdp:: delta-lambda
2421 increment per time step for lambda
2423 .. mdp:: init-lambda-state
2426 starting value for the lambda state (integer). Specifies which
2427 columm of the lambda vector (:mdp:`coul-lambdas`,
2428 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2429 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2430 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2431 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2432 the first column, and so on.
2434 .. mdp:: fep-lambdas
2437 Zero, one or more lambda values for which Delta H values will be
2438 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2439 steps. Values must be between 0 and 1. Free energy differences
2440 between different lambda values can then be determined with
2441 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2442 other -lambdas keywords because all components of the lambda vector
2443 that are not specified will use :mdp:`fep-lambdas` (including
2444 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2446 .. mdp:: coul-lambdas
2449 Zero, one or more lambda values for which Delta H values will be
2450 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2451 steps. Values must be between 0 and 1. Only the electrostatic
2452 interactions are controlled with this component of the lambda
2453 vector (and only if the lambda=0 and lambda=1 states have differing
2454 electrostatic interactions).
2456 .. mdp:: vdw-lambdas
2459 Zero, one or more lambda values for which Delta H values will be
2460 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2461 steps. Values must be between 0 and 1. Only the van der Waals
2462 interactions are controlled with this component of the lambda
2465 .. mdp:: bonded-lambdas
2468 Zero, one or more lambda values for which Delta H values will be
2469 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2470 steps. Values must be between 0 and 1. Only the bonded interactions
2471 are controlled with this component of the lambda vector.
2473 .. mdp:: restraint-lambdas
2476 Zero, one or more lambda values for which Delta H values will be
2477 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2478 steps. Values must be between 0 and 1. Only the restraint
2479 interactions: dihedral restraints, and the pull code restraints are
2480 controlled with this component of the lambda vector.
2482 .. mdp:: mass-lambdas
2485 Zero, one or more lambda values for which Delta H values will be
2486 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2487 steps. Values must be between 0 and 1. Only the particle masses are
2488 controlled with this component of the lambda vector.
2490 .. mdp:: temperature-lambdas
2493 Zero, one or more lambda values for which Delta H values will be
2494 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2495 steps. Values must be between 0 and 1. Only the temperatures
2496 controlled with this component of the lambda vector. Note that
2497 these lambdas should not be used for replica exchange, only for
2498 simulated tempering.
2500 .. mdp:: calc-lambda-neighbors
2503 Controls the number of lambda values for which Delta H values will
2504 be calculated and written out, if :mdp:`init-lambda-state` has
2505 been set. A positive value will limit the number of lambda points
2506 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2507 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2508 has a value of 2, energies for lambda points 3-7 will be calculated
2509 and writen out. A value of -1 means all lambda points will be
2510 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2511 1 is sufficient, while for MBAR -1 should be used.
2516 the soft-core alpha parameter, a value of 0 results in linear
2517 interpolation of the LJ and Coulomb interactions
2522 the power of the radial term in the soft-core equation. Possible
2523 values are 6 and 48. 6 is more standard, and is the default. When
2524 48 is used, then sc-alpha should generally be much lower (between
2530 Whether to apply the soft-core free energy interaction
2531 transformation to the Columbic interaction of a molecule. Default
2532 is no, as it is generally more efficient to turn off the Coulomic
2533 interactions linearly before turning off the van der Waals
2534 interactions. Note that it is only taken into account when lambda
2535 states are used, not with :mdp:`couple-lambda0` /
2536 :mdp:`couple-lambda1`, and you can still turn off soft-core
2537 interactions by setting :mdp:`sc-alpha` to 0.
2542 the power for lambda in the soft-core function, only the values 1
2548 the soft-core sigma for particles which have a C6 or C12 parameter
2549 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2551 .. mdp:: couple-moltype
2553 Here one can supply a molecule type (as defined in the topology)
2554 for calculating solvation or coupling free energies. There is a
2555 special option ``system`` that couples all molecule types in the
2556 system. This can be useful for equilibrating a system starting from
2557 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2558 on. The Van der Waals interactions and/or charges in this molecule
2559 type can be turned on or off between lambda=0 and lambda=1,
2560 depending on the settings of :mdp:`couple-lambda0` and
2561 :mdp:`couple-lambda1`. If you want to decouple one of several
2562 copies of a molecule, you need to copy and rename the molecule
2563 definition in the topology.
2565 .. mdp:: couple-lambda0
2567 .. mdp-value:: vdw-q
2569 all interactions are on at lambda=0
2573 the charges are zero (no Coulomb interactions) at lambda=0
2577 the Van der Waals interactions are turned at lambda=0; soft-core
2578 interactions will be required to avoid singularities
2582 the Van der Waals interactions are turned off and the charges
2583 are zero at lambda=0; soft-core interactions will be required to
2584 avoid singularities.
2586 .. mdp:: couple-lambda1
2588 analogous to :mdp:`couple-lambda1`, but for lambda=1
2590 .. mdp:: couple-intramol
2594 All intra-molecular non-bonded interactions for moleculetype
2595 :mdp:`couple-moltype` are replaced by exclusions and explicit
2596 pair interactions. In this manner the decoupled state of the
2597 molecule corresponds to the proper vacuum state without
2598 periodicity effects.
2602 The intra-molecular Van der Waals and Coulomb interactions are
2603 also turned on/off. This can be useful for partitioning
2604 free-energies of relatively large molecules, where the
2605 intra-molecular non-bonded interactions might lead to
2606 kinetically trapped vacuum conformations. The 1-4 pair
2607 interactions are not turned off.
2612 the frequency for writing dH/dlambda and possibly Delta H to
2613 dhdl.xvg, 0 means no ouput, should be a multiple of
2614 :mdp:`nstcalcenergy`.
2616 .. mdp:: dhdl-derivatives
2620 If yes (the default), the derivatives of the Hamiltonian with
2621 respect to lambda at each :mdp:`nstdhdl` step are written
2622 out. These values are needed for interpolation of linear energy
2623 differences with :ref:`gmx bar` (although the same can also be
2624 achieved with the right foreign lambda setting, that may not be as
2625 flexible), or with thermodynamic integration
2627 .. mdp:: dhdl-print-energy
2631 Include either the total or the potential energy in the dhdl
2632 file. Options are 'no', 'potential', or 'total'. This information
2633 is needed for later free energy analysis if the states of interest
2634 are at different temperatures. If all states are at the same
2635 temperature, this information is not needed. 'potential' is useful
2636 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2637 file. When rerunning from an existing trajectory, the kinetic
2638 energy will often not be correct, and thus one must compute the
2639 residual free energy from the potential alone, with the kinetic
2640 energy component computed analytically.
2642 .. mdp:: separate-dhdl-file
2646 The free energy values that are calculated (as specified with
2647 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2648 written out to a separate file, with the default name
2649 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2654 The free energy values are written out to the energy output file
2655 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2656 steps), where they can be extracted with :ref:`gmx energy` or
2657 used directly with :ref:`gmx bar`.
2659 .. mdp:: dh-hist-size
2662 If nonzero, specifies the size of the histogram into which the
2663 Delta H values (specified with foreign lambda) and the derivative
2664 dH/dl values are binned, and written to ener.edr. This can be used
2665 to save disk space while calculating free energy differences. One
2666 histogram gets written for each foreign lambda and two for the
2667 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2668 histogram settings (too small size or too wide bins) can introduce
2669 errors. Do not use histograms unless you're certain you need it.
2671 .. mdp:: dh-hist-spacing
2674 Specifies the bin width of the histograms, in energy units. Used in
2675 conjunction with :mdp:`dh-hist-size`. This size limits the
2676 accuracy with which free energies can be calculated. Do not use
2677 histograms unless you're certain you need it.
2680 Expanded Ensemble calculations
2681 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2683 .. mdp:: nstexpanded
2685 The number of integration steps beween attempted moves changing the
2686 system Hamiltonian in expanded ensemble simulations. Must be a
2687 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2694 No Monte Carlo in state space is performed.
2696 .. mdp-value:: metropolis-transition
2698 Uses the Metropolis weights to update the expanded ensemble
2699 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2702 .. mdp-value:: barker-transition
2704 Uses the Barker transition critera to update the expanded
2705 ensemble weight of each state i, defined by exp(-beta_new
2706 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2708 .. mdp-value:: wang-landau
2710 Uses the Wang-Landau algorithm (in state space, not energy
2711 space) to update the expanded ensemble weights.
2713 .. mdp-value:: min-variance
2715 Uses the minimum variance updating method of Escobedo et al. to
2716 update the expanded ensemble weights. Weights will not be the
2717 free energies, but will rather emphasize states that need more
2718 sampling to give even uncertainty.
2720 .. mdp:: lmc-mc-move
2724 No Monte Carlo in state space is performed.
2726 .. mdp-value:: metropolis-transition
2728 Randomly chooses a new state up or down, then uses the
2729 Metropolis critera to decide whether to accept or reject:
2730 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2732 .. mdp-value:: barker-transition
2734 Randomly chooses a new state up or down, then uses the Barker
2735 transition critera to decide whether to accept or reject:
2736 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2738 .. mdp-value:: gibbs
2740 Uses the conditional weights of the state given the coordinate
2741 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2744 .. mdp-value:: metropolized-gibbs
2746 Uses the conditional weights of the state given the coordinate
2747 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2748 to move to, EXCLUDING the current state, then uses a rejection
2749 step to ensure detailed balance. Always more efficient that
2750 Gibbs, though only marginally so in many situations, such as
2751 when only the nearest neighbors have decent phase space
2757 random seed to use for Monte Carlo moves in state space. When
2758 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2760 .. mdp:: mc-temperature
2762 Temperature used for acceptance/rejection for Monte Carlo moves. If
2763 not specified, the temperature of the simulation specified in the
2764 first group of :mdp:`ref-t` is used.
2769 The cutoff for the histogram of state occupancies to be reset, and
2770 the free energy incrementor to be changed from delta to delta *
2771 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2772 each histogram) / (average number of samples at each
2773 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2774 histogram is only considered flat if all Nratio > 0.8 AND
2775 simultaneously all 1/Nratio > 0.8.
2780 Each time the histogram is considered flat, then the current value
2781 of the Wang-Landau incrementor for the free energies is multiplied
2782 by :mdp:`wl-scale`. Value must be between 0 and 1.
2784 .. mdp:: init-wl-delta
2787 The initial value of the Wang-Landau incrementor in kT. Some value
2788 near 1 kT is usually most efficient, though sometimes a value of
2789 2-3 in units of kT works better if the free energy differences are
2792 .. mdp:: wl-oneovert
2795 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2796 the large sample limit. There is significant evidence that the
2797 standard Wang-Landau algorithms in state space presented here
2798 result in free energies getting 'burned in' to incorrect values
2799 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2800 then when the incrementor becomes less than 1/N, where N is the
2801 mumber of samples collected (and thus proportional to the data
2802 collection time, hence '1 over t'), then the Wang-Lambda
2803 incrementor is set to 1/N, decreasing every step. Once this occurs,
2804 :mdp:`wl-ratio` is ignored, but the weights will still stop
2805 updating when the equilibration criteria set in
2806 :mdp:`lmc-weights-equil` is achieved.
2808 .. mdp:: lmc-repeats
2811 Controls the number of times that each Monte Carlo swap type is
2812 performed each iteration. In the limit of large numbers of Monte
2813 Carlo repeats, then all methods converge to Gibbs sampling. The
2814 value will generally not need to be different from 1.
2816 .. mdp:: lmc-gibbsdelta
2819 Limit Gibbs sampling to selected numbers of neighboring states. For
2820 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2821 sampling over all of the states that are defined. A positive value
2822 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2823 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2824 value of -1 means that all states are considered. For less than 100
2825 states, it is probably not that expensive to include all states.
2827 .. mdp:: lmc-forced-nstart
2830 Force initial state space sampling to generate weights. In order to
2831 come up with reasonable initial weights, this setting allows the
2832 simulation to drive from the initial to the final lambda state,
2833 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2834 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2835 sufficiently long (thousands of steps, perhaps), then the weights
2836 will be close to correct. However, in most cases, it is probably
2837 better to simply run the standard weight equilibration algorithms.
2839 .. mdp:: nst-transition-matrix
2842 Frequency of outputting the expanded ensemble transition matrix. A
2843 negative number means it will only be printed at the end of the
2846 .. mdp:: symmetrized-transition-matrix
2849 Whether to symmetrize the empirical transition matrix. In the
2850 infinite limit the matrix will be symmetric, but will diverge with
2851 statistical noise for short timescales. Forced symmetrization, by
2852 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2853 like the existence of (small magnitude) negative eigenvalues.
2855 .. mdp:: mininum-var-min
2858 The min-variance strategy (option of :mdp:`lmc-stats` is only
2859 valid for larger number of samples, and can get stuck if too few
2860 samples are used at each state. :mdp:`mininum-var-min` is the
2861 minimum number of samples that each state that are allowed before
2862 the min-variance strategy is activated if selected.
2864 .. mdp:: init-lambda-weights
2866 The initial weights (free energies) used for the expanded ensemble
2867 states. Default is a vector of zero weights. format is similar to
2868 the lambda vector settings in :mdp:`fep-lambdas`, except the
2869 weights can be any floating point number. Units are kT. Its length
2870 must match the lambda vector lengths.
2872 .. mdp:: lmc-weights-equil
2876 Expanded ensemble weights continue to be updated throughout the
2881 The input expanded ensemble weights are treated as equilibrated,
2882 and are not updated throughout the simulation.
2884 .. mdp-value:: wl-delta
2886 Expanded ensemble weight updating is stopped when the
2887 Wang-Landau incrementor falls below this value.
2889 .. mdp-value:: number-all-lambda
2891 Expanded ensemble weight updating is stopped when the number of
2892 samples at all of the lambda states is greater than this value.
2894 .. mdp-value:: number-steps
2896 Expanded ensemble weight updating is stopped when the number of
2897 steps is greater than the level specified by this value.
2899 .. mdp-value:: number-samples
2901 Expanded ensemble weight updating is stopped when the number of
2902 total samples across all lambda states is greater than the level
2903 specified by this value.
2905 .. mdp-value:: count-ratio
2907 Expanded ensemble weight updating is stopped when the ratio of
2908 samples at the least sampled lambda state and most sampled
2909 lambda state greater than this value.
2911 .. mdp:: simulated-tempering
2914 Turn simulated tempering on or off. Simulated tempering is
2915 implemented as expanded ensemble sampling with different
2916 temperatures instead of different Hamiltonians.
2918 .. mdp:: sim-temp-low
2921 Low temperature for simulated tempering.
2923 .. mdp:: sim-temp-high
2926 High temperature for simulated tempering.
2928 .. mdp:: simulated-tempering-scaling
2930 Controls the way that the temperatures at intermediate lambdas are
2931 calculated from the :mdp:`temperature-lambdas` part of the lambda
2934 .. mdp-value:: linear
2936 Linearly interpolates the temperatures using the values of
2937 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2938 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2939 a temperature of 350. A nonlinear set of temperatures can always
2940 be implemented with uneven spacing in lambda.
2942 .. mdp-value:: geometric
2944 Interpolates temperatures geometrically between
2945 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2946 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2947 :mdp:`sim-temp-low`) raised to the power of
2948 (i/(ntemps-1)). This should give roughly equal exchange for
2949 constant heat capacity, though of course things simulations that
2950 involve protein folding have very high heat capacity peaks.
2952 .. mdp-value:: exponential
2954 Interpolates temperatures exponentially between
2955 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2956 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2957 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2958 (i))-1)/(exp(1.0)-i)).
2966 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2967 in groups Protein and Sol will experience constant acceleration as
2968 specified in the :mdp:`accelerate` line
2972 (0) [nm ps\ :sup:`-2`]
2973 acceleration for :mdp:`acc-grps`; x, y and z for each group
2974 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2975 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
2980 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2981 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2982 specifies for which dimension(s) the freezing applies. To avoid
2983 spurious contributions to the virial and pressure due to large
2984 forces between completely frozen atoms you need to use energy group
2985 exclusions, this also saves computing time. Note that coordinates
2986 of frozen atoms are not scaled by pressure-coupling algorithms.
2990 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2991 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
2992 N N N N`` means that particles in the first group can move only in
2993 Z direction. The particles in the second group can move in any
2996 .. mdp:: cos-acceleration
2998 (0) [nm ps\ :sup:`-2`]
2999 the amplitude of the acceleration profile for calculating the
3000 viscosity. The acceleration is in the X-direction and the magnitude
3001 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
3002 added to the energy file: the amplitude of the velocity profile and
3007 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
3008 The velocities of deformation for the box elements: a(x) b(y) c(z)
3009 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
3010 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
3011 elements are corrected for periodicity. The coordinates are
3012 transformed accordingly. Frozen degrees of freedom are (purposely)
3013 also transformed. The time ts is set to t at the first step and at
3014 steps at which x and v are written to trajectory to ensure exact
3015 restarts. Deformation can be used together with semiisotropic or
3016 anisotropic pressure coupling when the appropriate
3017 compressibilities are set to zero. The diagonal elements can be
3018 used to strain a solid. The off-diagonal elements can be used to
3019 shear a solid or a liquid.
3025 .. mdp:: electric-field-x
3026 .. mdp:: electric-field-y
3027 .. mdp:: electric-field-z
3029 Here you can specify an electric field that optionally can be
3030 alternating and pulsed. The general expression for the field
3031 has the form of a gaussian laser pulse:
3033 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
3035 For example, the four parameters for direction x are set in the
3036 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
3037 and ``electric-field-z``) like
3039 ``electric-field-x = E0 omega t0 sigma``
3041 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
3043 In the special case that ``sigma = 0``, the exponential term is omitted
3044 and only the cosine term is used. If also ``omega = 0`` a static
3045 electric field is applied.
3047 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
3050 Mixed quantum/classical molecular dynamics
3051 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3061 Do a QM/MM simulation. Several groups can be described at
3062 different QM levels separately. These are specified in the
3063 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
3064 initio* theory at which the groups are described is specified by
3065 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
3066 groups at different levels of theory is only possible with the
3067 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
3071 groups to be descibed at the QM level (works also in case of MiMiC QM/MM)
3075 .. mdp-value:: normal
3077 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
3078 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
3079 *ab initio* theory. The rest of the system is described at the
3080 MM level. The QM and MM subsystems interact as follows: MM point
3081 charges are included in the QM one-electron hamiltonian and all
3082 Lennard-Jones interactions are described at the MM level.
3084 .. mdp-value:: ONIOM
3086 The interaction between the subsystem is described using the
3087 ONIOM method by Morokuma and co-workers. There can be more than
3088 one :mdp:`QMMM-grps` each modeled at a different level of QM
3089 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
3094 Method used to compute the energy and gradients on the QM
3095 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
3096 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
3097 included in the active space is specified by :mdp:`CASelectrons`
3098 and :mdp:`CASorbitals`.
3103 Basis set used to expand the electronic wavefuntion. Only Gaussian
3104 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3105 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
3110 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
3111 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
3112 layer needs to be specified separately.
3117 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
3118 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
3119 needs to be specified separately.
3121 .. mdp:: CASorbitals
3124 The number of orbitals to be included in the active space when
3125 doing a CASSCF computation.
3127 .. mdp:: CASelectrons
3130 The number of electrons to be included in the active space when
3131 doing a CASSCF computation.
3137 No surface hopping. The system is always in the electronic
3142 Do a QM/MM MD simulation on the excited state-potential energy
3143 surface and enforce a *diabatic* hop to the ground-state when
3144 the system hits the conical intersection hyperline in the course
3145 the simulation. This option only works in combination with the
3149 Computational Electrophysiology
3150 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3151 Use these options to switch on and control ion/water position exchanges in "Computational
3152 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3158 Do not enable ion/water position exchanges.
3160 .. mdp-value:: X ; Y ; Z
3162 Allow for ion/water position exchanges along the chosen direction.
3163 In a typical setup with the membranes parallel to the x-y plane,
3164 ion/water pairs need to be exchanged in Z direction to sustain the
3165 requested ion concentrations in the compartments.
3167 .. mdp:: swap-frequency
3169 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3170 per compartment are determined and exchanges made if necessary.
3171 Normally it is not necessary to check at every time step.
3172 For typical Computational Electrophysiology setups, a value of about 100 is
3173 sufficient and yields a negligible performance impact.
3175 .. mdp:: split-group0
3177 Name of the index group of the membrane-embedded part of channel #0.
3178 The center of mass of these atoms defines one of the compartment boundaries
3179 and should be chosen such that it is near the center of the membrane.
3181 .. mdp:: split-group1
3183 Channel #1 defines the position of the other compartment boundary.
3185 .. mdp:: massw-split0
3187 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3191 Use the geometrical center.
3195 Use the center of mass.
3197 .. mdp:: massw-split1
3199 (no) As above, but for split-group #1.
3201 .. mdp:: solvent-group
3203 Name of the index group of solvent molecules.
3205 .. mdp:: coupl-steps
3207 (10) Average the number of ions per compartment over these many swap attempt steps.
3208 This can be used to prevent that ions near a compartment boundary
3209 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3213 (1) The number of different ion types to be controlled. These are during the
3214 simulation exchanged with solvent molecules to reach the desired reference numbers.
3216 .. mdp:: iontype0-name
3218 Name of the first ion type.
3220 .. mdp:: iontype0-in-A
3222 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3223 The default value of -1 means: use the number of ions as found in time step 0
3226 .. mdp:: iontype0-in-B
3228 (-1) Reference number of ions of type 0 for compartment B.
3230 .. mdp:: bulk-offsetA
3232 (0.0) Offset of the first swap layer from the compartment A midplane.
3233 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3234 at maximum distance (= bulk concentration) to the split group layers. However,
3235 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3236 towards one of the compartment-partitioning layers (at +/- 1.0).
3238 .. mdp:: bulk-offsetB
3240 (0.0) Offset of the other swap layer from the compartment B midplane.
3245 (\1) Only swap ions if threshold difference to requested count is reached.
3249 (2.0) [nm] Radius of the split cylinder #0.
3250 Two split cylinders (mimicking the channel pores) can optionally be defined
3251 relative to the center of the split group. With the help of these cylinders
3252 it can be counted which ions have passed which channel. The split cylinder
3253 definition has no impact on whether or not ion/water swaps are done.
3257 (1.0) [nm] Upper extension of the split cylinder #0.
3261 (1.0) [nm] Lower extension of the split cylinder #0.
3265 (2.0) [nm] Radius of the split cylinder #1.
3269 (1.0) [nm] Upper extension of the split cylinder #1.
3273 (1.0) [nm] Lower extension of the split cylinder #1.
3276 User defined thingies
3277 ^^^^^^^^^^^^^^^^^^^^^
3281 .. mdp:: userint1 (0)
3282 .. mdp:: userint2 (0)
3283 .. mdp:: userint3 (0)
3284 .. mdp:: userint4 (0)
3285 .. mdp:: userreal1 (0)
3286 .. mdp:: userreal2 (0)
3287 .. mdp:: userreal3 (0)
3288 .. mdp:: userreal4 (0)
3290 These you can use if you modify code. You can pass integers and
3291 reals and groups to your subroutine. Check the inputrec definition
3292 in ``src/gromacs/mdtypes/inputrec.h``
3297 These features have been removed from |Gromacs|, but so that old
3298 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3299 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3300 fatal error if this is set.
3306 .. mdp:: implicit-solvent
3310 .. _reference manual: gmx-manual-parent-dir_