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 the
567 :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`, this is by default set by the
568 :mdp:`verlet-buffer-tolerance` option and the value of
569 :mdp:`rlist` is ignored.
577 .. mdp-value:: Cut-off
579 Plain cut-off with pair list radius :mdp:`rlist` and
580 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
585 Classical Ewald sum electrostatics. The real-space cut-off
586 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
587 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
588 of wave vectors used in reciprocal space is controlled by
589 :mdp:`fourierspacing`. The relative accuracy of
590 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
592 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
593 large systems. It is included mainly for reference - in most
594 cases PME will perform much better.
598 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
599 space is similar to the Ewald sum, while the reciprocal part is
600 performed with FFTs. Grid dimensions are controlled with
601 :mdp:`fourierspacing` and the interpolation order with
602 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
603 interpolation the electrostatic forces have an accuracy of
604 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
605 this you might try 0.15 nm. When running in parallel the
606 interpolation parallelizes better than the FFT, so try
607 decreasing grid dimensions while increasing interpolation.
609 .. mdp-value:: P3M-AD
611 Particle-Particle Particle-Mesh algorithm with analytical
612 derivative for for long range electrostatic interactions. The
613 method and code is identical to SPME, except that the influence
614 function is optimized for the grid. This gives a slight increase
617 .. mdp-value:: Reaction-Field
619 Reaction field electrostatics with Coulomb cut-off
620 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
621 dielectric constant beyond the cut-off is
622 :mdp:`epsilon-rf`. The dielectric constant can be set to
623 infinity by setting :mdp:`epsilon-rf` =0.
625 .. mdp-value:: Reaction-Field-zero
627 In |Gromacs|, normal reaction-field electrostatics with
628 :mdp-value:`cutoff-scheme=group` leads to bad energy
629 conservation. :mdp-value:`coulombtype=Reaction-Field-zero` solves this by making
630 the potential zero beyond the cut-off. It can only be used with
631 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
632 only for that value the force vanishes at the
633 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
634 :mdp:`rcoulomb` to accommodate the size of charge groups
635 and diffusion between neighbor list updates. This, and the fact
636 that table lookups are used instead of analytical functions make
637 reaction-field-zero computationally more expensive than
638 normal reaction-field.
642 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
643 might want to use :mdp-value:`coulombtype=Reaction-Field-zero` instead, which has
644 a similar potential shape, but has a physical interpretation and
645 has better energies due to the exclusion correction terms.
647 .. mdp-value:: Encad-Shift
649 The Coulomb potential is decreased over the whole range, using
650 the definition from the Encad simulation package.
652 .. mdp-value:: Switch
654 Analogous to :mdp-value:`vdwtype=Switch` for
655 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
656 serious artifacts, advice: use :mdp-value:`coulombtype=Reaction-Field-zero`
661 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
662 with user-defined potential functions for repulsion, dispersion
663 and Coulomb. When pair interactions are present, :ref:`gmx
664 mdrun` also expects to find a file ``tablep.xvg`` for the pair
665 interactions. When the same interactions should be used for
666 non-bonded and pair interactions the user can specify the same
667 file name for both table files. These files should contain 7
668 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
669 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
670 function, ``g(x)`` the dispersion function and ``h(x)`` the
671 repulsion function. When :mdp:`vdwtype` is not set to User the
672 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
673 the non-bonded interactions ``x`` values should run from 0 to
674 the largest cut-off distance + :mdp:`table-extension` and
675 should be uniformly spaced. For the pair interactions the table
676 length in the file will be used. The optimal spacing, which is
677 used for non-user tables, is ``0.002 nm`` when you run in mixed
678 precision or ``0.0005 nm`` when you run in double precision. The
679 function value at ``x=0`` is not important. More information is
680 in the printed manual.
682 .. mdp-value:: PME-Switch
684 A combination of PME and a switch function for the direct-space
685 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
686 :mdp:`rlist`. This is mainly useful constant energy simulations
687 (note that using PME with :mdp-value:`cutoff-scheme=Verlet`
688 will be more efficient).
690 .. mdp-value:: PME-User
692 A combination of PME and user tables (see
693 above). :mdp:`rcoulomb` is allowed to be smaller than
694 :mdp:`rlist`. The PME mesh contribution is subtracted from the
695 user table by :ref:`gmx mdrun`. Because of this subtraction the
696 user tables should contain about 10 decimal places.
698 .. mdp-value:: PME-User-Switch
700 A combination of PME-User and a switching function (see
701 above). The switching function is applied to final
702 particle-particle interaction, *i.e.* both to the user supplied
703 function and the PME Mesh correction part.
705 .. mdp:: coulomb-modifier
707 .. mdp-value:: Potential-shift
709 Shift the Coulomb potential by a constant such that it is zero
710 at the cut-off. This makes the potential the integral of the
711 force. Note that this does not affect the forces or the
716 Use an unmodified Coulomb potential. This can be useful
717 when comparing energies with those computed with other software.
719 .. mdp:: rcoulomb-switch
722 where to start switching the Coulomb potential, only relevant
723 when force or potential switching is used
728 The distance for the Coulomb cut-off. Note that with PME this value
729 can be increased by the PME tuning in :ref:`gmx mdrun` along with
730 the PME grid spacing.
735 The relative dielectric constant. A value of 0 means infinity.
740 The relative dielectric constant of the reaction field. This
741 is only used with reaction-field electrostatics. A value of 0
750 .. mdp-value:: Cut-off
752 Plain cut-off with pair list radius :mdp:`rlist` and VdW
753 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
757 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
758 grid dimensions are controlled with :mdp:`fourierspacing` in
759 the same way as for electrostatics, and the interpolation order
760 is controlled with :mdp:`pme-order`. The relative accuracy of
761 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
762 and the specific combination rules that are to be used by the
763 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
767 This functionality is deprecated and replaced by using
768 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
769 The LJ (not Buckingham) potential is decreased over the whole range and
770 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
771 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
772 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
773 size of charge groups and diffusion between neighbor list
776 .. mdp-value:: Switch
778 This functionality is deprecated and replaced by using
779 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
780 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
781 which it is switched off to reach zero at :mdp:`rvdw`. Both the
782 potential and force functions are continuously smooth, but be
783 aware that all switch functions will give rise to a bulge
784 (increase) in the force (since we are switching the
785 potential). The neighbor search cut-off :mdp:`rlist` should be
786 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
787 size of charge groups and diffusion between neighbor list
790 .. mdp-value:: Encad-Shift
792 The LJ (not Buckingham) potential is decreased over the whole
793 range, using the definition from the Encad simulation package.
797 See user for :mdp:`coulombtype`. The function value at zero is
798 not important. When you want to use LJ correction, make sure
799 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
800 function. When :mdp:`coulombtype` is not set to User the values
801 for the ``f`` and ``-f'`` columns are ignored.
803 .. mdp:: vdw-modifier
805 .. mdp-value:: Potential-shift
807 Shift the Van der Waals potential by a constant such that it is
808 zero at the cut-off. This makes the potential the integral of
809 the force. Note that this does not affect the forces or the
814 Use an unmodified Van der Waals potential. This can be useful
815 when comparing energies with those computed with other software.
817 .. mdp-value:: Force-switch
819 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
820 and :mdp:`rvdw`. This shifts the potential shift over the whole
821 range and switches it to zero at the cut-off. Note that this is
822 more expensive to calculate than a plain cut-off and it is not
823 required for energy conservation, since Potential-shift
824 conserves energy just as well.
826 .. mdp-value:: Potential-switch
828 Smoothly switches the potential to zero between
829 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
830 articifically large forces in the switching region and is much
831 more expensive to calculate. This option should only be used if
832 the force field you are using requires this.
837 where to start switching the LJ force and possibly the potential,
838 only relevant when force or potential switching is used
843 distance for the LJ or Buckingham cut-off
849 don't apply any correction
851 .. mdp-value:: EnerPres
853 apply long range dispersion corrections for Energy and Pressure
857 apply long range dispersion corrections for Energy only
863 .. mdp:: table-extension
866 Extension of the non-bonded potential lookup tables beyond the
867 largest cut-off distance. The value should be large enough to
868 account for charge group sizes and the diffusion between
869 neighbor-list updates. Without user defined potential the same
870 table length is used for the lookup tables for the 1-4
871 interactions, which are always tabulated irrespective of the use of
872 tables for the non-bonded interactions. The value of
873 :mdp:`table-extension` in no way affects the values of
874 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
876 .. mdp:: energygrp-table
878 When user tables are used for electrostatics and/or VdW, here one
879 can give pairs of energy groups for which seperate user tables
880 should be used. The two energy groups will be appended to the table
881 file name, in order of their definition in :mdp:`energygrps`,
882 seperated by underscores. For example, if ``energygrps = Na Cl
883 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
884 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
885 normal ``table.xvg`` which will be used for all other energy group
892 .. mdp:: fourierspacing
895 For ordinary Ewald, the ratio of the box dimensions and the spacing
896 determines a lower bound for the number of wave vectors to use in
897 each (signed) direction. For PME and P3M, that ratio determines a
898 lower bound for the number of Fourier-space grid points that will
899 be used along that axis. In all cases, the number for each
900 direction can be overridden by entering a non-zero value for that
901 :mdp:`fourier-nx` direction. For optimizing the relative load of
902 the particle-particle interactions and the mesh part of PME, it is
903 useful to know that the accuracy of the electrostatics remains
904 nearly constant when the Coulomb cut-off and the PME grid spacing
905 are scaled by the same factor. Note that this spacing can be scaled
906 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
913 Highest magnitude of wave vectors in reciprocal space when using Ewald.
914 Grid size when using PME or P3M. These values override
915 :mdp:`fourierspacing` per direction. The best choice is powers of
916 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
917 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
923 Interpolation order for PME. 4 equals cubic interpolation. You
924 might try 6/8/10 when running in parallel and simultaneously
925 decrease grid dimension.
930 The relative strength of the Ewald-shifted direct potential at
931 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
932 will give a more accurate direct sum, but then you need more wave
933 vectors for the reciprocal sum.
935 .. mdp:: ewald-rtol-lj
938 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
939 to control the relative strength of the dispersion potential at
940 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
941 electrostatic potential.
943 .. mdp:: lj-pme-comb-rule
946 The combination rules used to combine VdW-parameters in the
947 reciprocal part of LJ-PME. Geometric rules are much faster than
948 Lorentz-Berthelot and usually the recommended choice, even when the
949 rest of the force field uses the Lorentz-Berthelot rules.
951 .. mdp-value:: Geometric
953 Apply geometric combination rules
955 .. mdp-value:: Lorentz-Berthelot
957 Apply Lorentz-Berthelot combination rules
959 .. mdp:: ewald-geometry
963 The Ewald sum is performed in all three dimensions.
967 The reciprocal sum is still performed in 3D, but a force and
968 potential correction applied in the `z` dimension to produce a
969 pseudo-2D summation. If your system has a slab geometry in the
970 `x-y` plane you can try to increase the `z`-dimension of the box
971 (a box height of 3 times the slab height is usually ok) and use
974 .. mdp:: epsilon-surface
977 This controls the dipole correction to the Ewald summation in
978 3D. The default value of zero means it is turned off. Turn it on by
979 setting it to the value of the relative permittivity of the
980 imaginary surface around your infinite system. Be careful - you
981 shouldn't use this if you have free mobile charges in your
982 system. This value does not affect the slab 3DC variant of the long
993 No temperature coupling.
995 .. mdp-value:: berendsen
997 Temperature coupling with a Berendsen thermostat to a bath with
998 temperature :mdp:`ref-t`, with time constant
999 :mdp:`tau-t`. Several groups can be coupled separately, these
1000 are specified in the :mdp:`tc-grps` field separated by spaces.
1002 .. mdp-value:: nose-hoover
1004 Temperature coupling using a Nose-Hoover extended ensemble. The
1005 reference temperature and coupling groups are selected as above,
1006 but in this case :mdp:`tau-t` controls the period of the
1007 temperature fluctuations at equilibrium, which is slightly
1008 different from a relaxation time. For NVT simulations the
1009 conserved energy quantity is written to the energy and log files.
1011 .. mdp-value:: andersen
1013 Temperature coupling by randomizing a fraction of the particle velocities
1014 at each timestep. Reference temperature and coupling groups are
1015 selected as above. :mdp:`tau-t` is the average time between
1016 randomization of each molecule. Inhibits particle dynamics
1017 somewhat, but little or no ergodicity issues. Currently only
1018 implemented with velocity Verlet, and not implemented with
1021 .. mdp-value:: andersen-massive
1023 Temperature coupling by randomizing velocities of all particles at
1024 infrequent timesteps. Reference temperature and coupling groups are
1025 selected as above. :mdp:`tau-t` is the time between
1026 randomization of all molecules. Inhibits particle dynamics
1027 somewhat, but little or no ergodicity issues. Currently only
1028 implemented with velocity Verlet.
1030 .. mdp-value:: v-rescale
1032 Temperature coupling using velocity rescaling with a stochastic
1033 term (JCP 126, 014101). This thermostat is similar to Berendsen
1034 coupling, with the same scaling using :mdp:`tau-t`, but the
1035 stochastic term ensures that a proper canonical ensemble is
1036 generated. The random seed is set with :mdp:`ld-seed`. This
1037 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1038 simulations the conserved energy quantity is written to the
1039 energy and log file.
1044 The frequency for coupling the temperature. The default value of -1
1045 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1046 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1047 Verlet integrators :mdp:`nsttcouple` is set to 1.
1049 .. mdp:: nh-chain-length
1052 The number of chained Nose-Hoover thermostats for velocity Verlet
1053 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1054 only supports 1. Data for the NH chain variables is not printed
1055 to the :ref:`edr` file by default, but can be turned on with the
1056 :mdp:`print-nose-hoover-chain-variables` option.
1058 .. mdp:: print-nose-hoover-chain-variables
1062 Do not store Nose-Hoover chain variables in the energy file.
1066 Store all positions and velocities of the Nose-Hoover chain
1071 groups to couple to separate temperature baths
1076 time constant for coupling (one for each group in
1077 :mdp:`tc-grps`), -1 means no temperature coupling
1082 reference temperature for coupling (one for each group in
1093 No pressure coupling. This means a fixed box size.
1095 .. mdp-value:: Berendsen
1097 Exponential relaxation pressure coupling with time constant
1098 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1099 argued that this does not yield a correct thermodynamic
1100 ensemble, but it is the most efficient way to scale a box at the
1103 .. mdp-value:: Parrinello-Rahman
1105 Extended-ensemble pressure coupling where the box vectors are
1106 subject to an equation of motion. The equation of motion for the
1107 atoms is coupled to this. No instantaneous scaling takes
1108 place. As for Nose-Hoover temperature coupling the time constant
1109 :mdp:`tau-p` is the period of pressure fluctuations at
1110 equilibrium. This is probably a better method when you want to
1111 apply pressure scaling during data collection, but beware that
1112 you can get very large oscillations if you are starting from a
1113 different pressure. For simulations where the exact fluctations
1114 of the NPT ensemble are important, or if the pressure coupling
1115 time is very short it may not be appropriate, as the previous
1116 time step pressure is used in some steps of the |Gromacs|
1117 implementation for the current time step pressure.
1121 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1122 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1123 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1124 time constant :mdp:`tau-p` is the period of pressure
1125 fluctuations at equilibrium. This is probably a better method
1126 when you want to apply pressure scaling during data collection,
1127 but beware that you can get very large oscillations if you are
1128 starting from a different pressure. Currently (as of version
1129 5.1), it only supports isotropic scaling, and only works without
1134 Specifies the kind of isotropy of the pressure coupling used. Each
1135 kind takes one or more values for :mdp:`compressibility` and
1136 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1138 .. mdp-value:: isotropic
1140 Isotropic pressure coupling with time constant
1141 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1142 :mdp:`ref-p` is required.
1144 .. mdp-value:: semiisotropic
1146 Pressure coupling which is isotropic in the ``x`` and ``y``
1147 direction, but different in the ``z`` direction. This can be
1148 useful for membrane simulations. Two values each for
1149 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1150 ``x/y`` and ``z`` directions respectively.
1152 .. mdp-value:: anisotropic
1154 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1155 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1156 respectively. When the off-diagonal compressibilities are set to
1157 zero, a rectangular box will stay rectangular. Beware that
1158 anisotropic scaling can lead to extreme deformation of the
1161 .. mdp-value:: surface-tension
1163 Surface tension coupling for surfaces parallel to the
1164 xy-plane. Uses normal pressure coupling for the `z`-direction,
1165 while the surface tension is coupled to the `x/y` dimensions of
1166 the box. The first :mdp:`ref-p` value is the reference surface
1167 tension times the number of surfaces ``bar nm``, the second
1168 value is the reference `z`-pressure ``bar``. The two
1169 :mdp:`compressibility` values are the compressibility in the
1170 `x/y` and `z` direction respectively. The value for the
1171 `z`-compressibility should be reasonably accurate since it
1172 influences the convergence of the surface-tension, it can also
1173 be set to zero to have a box with constant height.
1178 The frequency for coupling the pressure. The default value of -1
1179 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1180 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1181 Verlet integrators :mdp:`nstpcouple` is set to 1.
1186 The time constant for pressure coupling (one value for all
1189 .. mdp:: compressibility
1192 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1193 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1194 required values is implied by :mdp:`pcoupltype`.
1199 The reference pressure for coupling. The number of required values
1200 is implied by :mdp:`pcoupltype`.
1202 .. mdp:: refcoord-scaling
1206 The reference coordinates for position restraints are not
1207 modified. Note that with this option the virial and pressure
1208 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1213 The reference coordinates are scaled with the scaling matrix of
1214 the pressure coupling.
1218 Scale the center of mass of the reference coordinates with the
1219 scaling matrix of the pressure coupling. The vectors of each
1220 reference coordinate to the center of mass are not scaled. Only
1221 one COM is used, even when there are multiple molecules with
1222 position restraints. For calculating the COM of the reference
1223 coordinates in the starting configuration, periodic boundary
1224 conditions are not taken into account. Note that with this option
1225 the virial and pressure might be ill defined, see
1226 :ref:`here <reference-manual-position-restraints>` for more details.
1232 Simulated annealing is controlled separately for each temperature
1233 group in |Gromacs|. The reference temperature is a piecewise linear
1234 function, but you can use an arbitrary number of points for each
1235 group, and choose either a single sequence or a periodic behaviour for
1236 each group. The actual annealing is performed by dynamically changing
1237 the reference temperature used in the thermostat algorithm selected,
1238 so remember that the system will usually not instantaneously reach the
1239 reference temperature!
1243 Type of annealing for each temperature group
1247 No simulated annealing - just couple to reference temperature value.
1249 .. mdp-value:: single
1251 A single sequence of annealing points. If your simulation is
1252 longer than the time of the last point, the temperature will be
1253 coupled to this constant value after the annealing sequence has
1254 reached the last time point.
1256 .. mdp-value:: periodic
1258 The annealing will start over at the first reference point once
1259 the last reference time is reached. This is repeated until the
1262 .. mdp:: annealing-npoints
1264 A list with the number of annealing reference/control points used
1265 for each temperature group. Use 0 for groups that are not
1266 annealed. The number of entries should equal the number of
1269 .. mdp:: annealing-time
1271 List of times at the annealing reference/control points for each
1272 group. If you are using periodic annealing, the times will be used
1273 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1274 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1275 etc. The number of entries should equal the sum of the numbers
1276 given in :mdp:`annealing-npoints`.
1278 .. mdp:: annealing-temp
1280 List of temperatures at the annealing reference/control points for
1281 each group. The number of entries should equal the sum of the
1282 numbers given in :mdp:`annealing-npoints`.
1284 Confused? OK, let's use an example. Assume you have two temperature
1285 groups, set the group selections to ``annealing = single periodic``,
1286 the number of points of each group to ``annealing-npoints = 3 4``, the
1287 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1288 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1289 will be coupled to 298K at 0ps, but the reference temperature will
1290 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1291 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1292 second group is coupled to 298K at 0ps, it increases linearly to 320K
1293 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1294 decreases to 298K, and then it starts over with the same pattern
1295 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1296 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1306 Do not generate velocities. The velocities are set to zero
1307 when there are no velocities in the input structure file.
1311 Generate velocities in :ref:`gmx grompp` according to a
1312 Maxwell distribution at temperature :mdp:`gen-temp`, with
1313 random seed :mdp:`gen-seed`. This is only meaningful with
1314 :mdp-value:`integrator=md`.
1319 temperature for Maxwell distribution
1324 used to initialize random generator for random velocities,
1325 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1332 .. mdp:: constraints
1334 Controls which bonds in the topology will be converted to rigid
1335 holonomic constraints. Note that typical rigid water models do not
1336 have bonds, but rather a specialized ``[settles]`` directive, so
1337 are not affected by this keyword.
1341 No bonds converted to constraints.
1343 .. mdp-value:: h-bonds
1345 Convert the bonds with H-atoms to constraints.
1347 .. mdp-value:: all-bonds
1349 Convert all bonds to constraints.
1351 .. mdp-value:: h-angles
1353 Convert all bonds to constraints and convert the angles that
1354 involve H-atoms to bond-constraints.
1356 .. mdp-value:: all-angles
1358 Convert all bonds to constraints and all angles to bond-constraints.
1360 .. mdp:: constraint-algorithm
1362 Chooses which solver satisfies any non-SETTLE holonomic
1365 .. mdp-value:: LINCS
1367 LINear Constraint Solver. With domain decomposition the parallel
1368 version P-LINCS is used. The accuracy in set with
1369 :mdp:`lincs-order`, which sets the number of matrices in the
1370 expansion for the matrix inversion. After the matrix inversion
1371 correction the algorithm does an iterative correction to
1372 compensate for lengthening due to rotation. The number of such
1373 iterations can be controlled with :mdp:`lincs-iter`. The root
1374 mean square relative constraint deviation is printed to the log
1375 file every :mdp:`nstlog` steps. If a bond rotates more than
1376 :mdp:`lincs-warnangle` in one step, a warning will be printed
1377 both to the log file and to ``stderr``. LINCS should not be used
1378 with coupled angle constraints.
1380 .. mdp-value:: SHAKE
1382 SHAKE is slightly slower and less stable than LINCS, but does
1383 work with angle constraints. The relative tolerance is set with
1384 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1385 does not support constraints between atoms on different nodes,
1386 thus it can not be used with domain decompositon when inter
1387 charge-group constraints are present. SHAKE can not be used with
1388 energy minimization.
1390 .. mdp:: continuation
1392 This option was formerly known as ``unconstrained-start``.
1396 apply constraints to the start configuration and reset shells
1400 do not apply constraints to the start configuration and do not
1401 reset shells, useful for exact coninuation and reruns
1406 relative tolerance for SHAKE
1408 .. mdp:: lincs-order
1411 Highest order in the expansion of the constraint coupling
1412 matrix. When constraints form triangles, an additional expansion of
1413 the same order is applied on top of the normal expansion only for
1414 the couplings within such triangles. For "normal" MD simulations an
1415 order of 4 usually suffices, 6 is needed for large time-steps with
1416 virtual sites or BD. For accurate energy minimization an order of 8
1417 or more might be required. With domain decomposition, the cell size
1418 is limited by the distance spanned by :mdp:`lincs-order` +1
1419 constraints. When one wants to scale further than this limit, one
1420 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1421 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1422 )* :mdp:`lincs-order` remains constant.
1427 Number of iterations to correct for rotational lengthening in
1428 LINCS. For normal runs a single step is sufficient, but for NVE
1429 runs where you want to conserve energy accurately or for accurate
1430 energy minimization you might want to increase it to 2.
1432 .. mdp:: lincs-warnangle
1435 maximum angle that a bond can rotate before LINCS will complain
1441 bonds are represented by a harmonic potential
1445 bonds are represented by a Morse potential
1448 Energy group exclusions
1449 ^^^^^^^^^^^^^^^^^^^^^^^
1451 .. mdp:: energygrp-excl
1453 Pairs of energy groups for which all non-bonded interactions are
1454 excluded. An example: if you have two energy groups ``Protein`` and
1455 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1456 would give only the non-bonded interactions between the protein and
1457 the solvent. This is especially useful for speeding up energy
1458 calculations with ``mdrun -rerun`` and for excluding interactions
1459 within frozen groups.
1468 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1469 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1470 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1471 used (it is usually best to use semiisotropic pressure coupling
1472 with the ``x/y`` compressibility set to 0, as otherwise the surface
1473 area will change). Walls interact wit the rest of the system
1474 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1475 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1476 monitor the interaction of energy groups with each wall. The center
1477 of mass motion removal will be turned off in the ``z``-direction.
1479 .. mdp:: wall-atomtype
1481 the atom type name in the force field for each wall. By (for
1482 example) defining a special wall atom type in the topology with its
1483 own combination rules, this allows for independent tuning of the
1484 interaction of each atomtype with the walls.
1490 LJ integrated over the volume behind the wall: 9-3 potential
1494 LJ integrated over the wall surface: 10-4 potential
1498 direct LJ potential with the ``z`` distance from the wall
1502 user defined potentials indexed with the ``z`` distance from the
1503 wall, the tables are read analogously to the
1504 :mdp:`energygrp-table` option, where the first name is for a
1505 "normal" energy group and the second name is ``wall0`` or
1506 ``wall1``, only the dispersion and repulsion columns are used
1508 .. mdp:: wall-r-linpot
1511 Below this distance from the wall the potential is continued
1512 linearly and thus the force is constant. Setting this option to a
1513 postive value is especially useful for equilibration when some
1514 atoms are beyond a wall. When the value is <=0 (<0 for
1515 :mdp:`wall-type` =table), a fatal error is generated when atoms
1518 .. mdp:: wall-density
1520 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1521 the number density of the atoms for each wall for wall types 9-3
1524 .. mdp:: wall-ewald-zfac
1527 The scaling factor for the third box vector for Ewald summation
1528 only, the minimum is 2. Ewald summation can only be used with
1529 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1530 ``=3dc``. The empty layer in the box serves to decrease the
1531 unphysical Coulomb interaction between periodic images.
1537 Note that where pulling coordinates are applicable, there can be more
1538 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1539 variables will exist accordingly. Documentation references to things
1540 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1541 applicable pulling coordinate, eg. the second pull coordinate is described by
1542 pull-coord2-vec, pull-coord2-k, and so on.
1548 No center of mass pulling. All the following pull options will
1549 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1554 Center of mass pulling will be applied on 1 or more groups using
1555 1 or more pull coordinates.
1557 .. mdp:: pull-cylinder-r
1560 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1562 .. mdp:: pull-constr-tol
1565 the relative constraint tolerance for constraint pulling
1567 .. mdp:: pull-print-com
1571 do not print the COM for any group
1575 print the COM of all groups for all pull coordinates
1577 .. mdp:: pull-print-ref-value
1581 do not print the reference value for each pull coordinate
1585 print the reference value for each pull coordinate
1587 .. mdp:: pull-print-components
1591 only print the distance for each pull coordinate
1595 print the distance and Cartesian components selected in
1596 :mdp:`pull-coord1-dim`
1598 .. mdp:: pull-nstxout
1601 frequency for writing out the COMs of all the pull group (0 is
1604 .. mdp:: pull-nstfout
1607 frequency for writing out the force of all the pulled group
1610 .. mdp:: pull-pbc-ref-prev-step-com
1614 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1615 treatment of periodic boundary conditions.
1619 Use the COM of the previous step as reference for the treatment
1620 of periodic boundary conditions. The reference is initialized
1621 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1622 be located centrally in the group. Using the COM from the
1623 previous step can be useful if one or more pull groups are large.
1625 .. mdp:: pull-xout-average
1629 Write the instantaneous coordinates for all the pulled groups.
1633 Write the average coordinates (since last output) for all the
1634 pulled groups. N.b., some analysis tools might expect instantaneous
1637 .. mdp:: pull-fout-average
1641 Write the instantaneous force for all the pulled groups.
1645 Write the average force (since last output) for all the
1646 pulled groups. N.b., some analysis tools might expect instantaneous
1649 .. mdp:: pull-ngroups
1652 The number of pull groups, not including the absolute reference
1653 group, when used. Pull groups can be reused in multiple pull
1654 coordinates. Below only the pull options for group 1 are given,
1655 further groups simply increase the group index number.
1657 .. mdp:: pull-ncoords
1660 The number of pull coordinates. Below only the pull options for
1661 coordinate 1 are given, further coordinates simply increase the
1662 coordinate index number.
1664 .. mdp:: pull-group1-name
1666 The name of the pull group, is looked up in the index file or in
1667 the default groups to obtain the atoms involved.
1669 .. mdp:: pull-group1-weights
1671 Optional relative weights which are multiplied with the masses of
1672 the atoms to give the total weight for the COM. The number should
1673 be 0, meaning all 1, or the number of atoms in the pull group.
1675 .. mdp:: pull-group1-pbcatom
1678 The reference atom for the treatment of periodic boundary
1679 conditions inside the group (this has no effect on the treatment of
1680 the pbc between groups). This option is only important when the
1681 diameter of the pull group is larger than half the shortest box
1682 vector. For determining the COM, all atoms in the group are put at
1683 their periodic image which is closest to
1684 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1685 atom (number wise) is used, which is only safe for small groups.
1686 :ref:`gmx grompp` checks that the maximum distance from the reference
1687 atom (specifically chosen, or not) to the other atoms in the group
1688 is not too large. This parameter is not used with
1689 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1690 weighting, which is useful for a group of molecules in a periodic
1691 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1694 .. mdp:: pull-coord1-type
1696 .. mdp-value:: umbrella
1698 Center of mass pulling using an umbrella potential between the
1699 reference group and one or more groups.
1701 .. mdp-value:: constraint
1703 Center of mass pulling using a constraint between the reference
1704 group and one or more groups. The setup is identical to the
1705 option umbrella, except for the fact that a rigid constraint is
1706 applied instead of a harmonic potential.
1708 .. mdp-value:: constant-force
1710 Center of mass pulling using a linear potential and therefore a
1711 constant force. For this option there is no reference position
1712 and therefore the parameters :mdp:`pull-coord1-init` and
1713 :mdp:`pull-coord1-rate` are not used.
1715 .. mdp-value:: flat-bottom
1717 At distances above :mdp:`pull-coord1-init` a harmonic potential
1718 is applied, otherwise no potential is applied.
1720 .. mdp-value:: flat-bottom-high
1722 At distances below :mdp:`pull-coord1-init` a harmonic potential
1723 is applied, otherwise no potential is applied.
1725 .. mdp-value:: external-potential
1727 An external potential that needs to be provided by another
1730 .. mdp:: pull-coord1-potential-provider
1732 The name of the external module that provides the potential for
1733 the case where :mdp:`pull-coord1-type` is external-potential.
1735 .. mdp:: pull-coord1-geometry
1737 .. mdp-value:: distance
1739 Pull along the vector connecting the two groups. Components can
1740 be selected with :mdp:`pull-coord1-dim`.
1742 .. mdp-value:: direction
1744 Pull in the direction of :mdp:`pull-coord1-vec`.
1746 .. mdp-value:: direction-periodic
1748 As :mdp-value:`pull-coord1-geometry=direction`, but allows the distance to be larger
1749 than half the box size. With this geometry the box should not be
1750 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1751 the pull force is not added to virial.
1753 .. mdp-value:: direction-relative
1755 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1756 that points from the COM of a third to the COM of a fourth pull
1757 group. This means that 4 groups need to be supplied in
1758 :mdp:`pull-coord1-groups`. Note that the pull force will give
1759 rise to a torque on the pull vector, which is turn leads to
1760 forces perpendicular to the pull vector on the two groups
1761 defining the vector. If you want a pull group to move between
1762 the two groups defining the vector, simply use the union of
1763 these two groups as the reference group.
1765 .. mdp-value:: cylinder
1767 Designed for pulling with respect to a layer where the reference
1768 COM is given by a local cylindrical part of the reference group.
1769 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1770 the first of the two groups in :mdp:`pull-coord1-groups` a
1771 cylinder is selected around the axis going through the COM of
1772 the second group with direction :mdp:`pull-coord1-vec` with
1773 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1774 continously to zero as the radial distance goes from 0 to
1775 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1776 dependence gives rise to radial forces on both pull groups.
1777 Note that the radius should be smaller than half the box size.
1778 For tilted cylinders they should be even smaller than half the
1779 box size since the distance of an atom in the reference group
1780 from the COM of the pull group has both a radial and an axial
1781 component. This geometry is not supported with constraint
1784 .. mdp-value:: angle
1786 Pull along an angle defined by four groups. The angle is
1787 defined as the angle between two vectors: the vector connecting
1788 the COM of the first group to the COM of the second group and
1789 the vector connecting the COM of the third group to the COM of
1792 .. mdp-value:: angle-axis
1794 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1795 Thus, only the two groups that define the first vector need to be given.
1797 .. mdp-value:: dihedral
1799 Pull along a dihedral angle defined by six groups. These pairwise
1800 define three vectors: the vector connecting the COM of group 1
1801 to the COM of group 2, the COM of group 3 to the COM of group 4,
1802 and the COM of group 5 to the COM group 6. The dihedral angle is
1803 then defined as the angle between two planes: the plane spanned by the
1804 the two first vectors and the plane spanned the two last vectors.
1807 .. mdp:: pull-coord1-groups
1809 The group indices on which this pull coordinate will operate.
1810 The number of group indices required is geometry dependent.
1811 The first index can be 0, in which case an
1812 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1813 absolute reference the system is no longer translation invariant
1814 and one should think about what to do with the center of mass
1817 .. mdp:: pull-coord1-dim
1820 Selects the dimensions that this pull coordinate acts on and that
1821 are printed to the output files when
1822 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1823 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1824 components set to Y contribute to the distance. Thus setting this
1825 to Y Y N results in a distance in the x/y plane. With other
1826 geometries all dimensions with non-zero entries in
1827 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1828 dimensions only affect the output.
1830 .. mdp:: pull-coord1-origin
1833 The pull reference position for use with an absolute reference.
1835 .. mdp:: pull-coord1-vec
1838 The pull direction. :ref:`gmx grompp` normalizes the vector.
1840 .. mdp:: pull-coord1-start
1844 do not modify :mdp:`pull-coord1-init`
1848 add the COM distance of the starting conformation to
1849 :mdp:`pull-coord1-init`
1851 .. mdp:: pull-coord1-init
1854 The reference distance or reference angle at t=0.
1856 .. mdp:: pull-coord1-rate
1858 (0) [nm/ps] or [deg/ps]
1859 The rate of change of the reference position or reference angle.
1861 .. mdp:: pull-coord1-k
1863 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1864 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1865 The force constant. For umbrella pulling this is the harmonic force
1866 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1867 for angles). For constant force pulling this is the
1868 force constant of the linear potential, and thus the negative (!)
1869 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1870 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1871 Note that for angles the force constant is expressed in terms of radians
1872 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1874 .. mdp:: pull-coord1-kB
1876 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1877 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1878 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1879 :mdp:`free-energy` is turned on. The force constant is then (1 -
1880 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1882 AWH adaptive biasing
1883 ^^^^^^^^^^^^^^^^^^^^
1893 Adaptively bias a reaction coordinate using the AWH method and estimate
1894 the corresponding PMF. The PMF and other AWH data are written to energy
1895 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1896 the ``gmx awh`` tool. The AWH coordinate can be
1897 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1898 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1899 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1900 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1902 .. mdp:: awh-potential
1904 .. mdp-value:: convolved
1906 The applied biasing potential is the convolution of the bias function and a
1907 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1908 in a smooth potential function and force. The resolution of the potential is set
1909 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1911 .. mdp-value:: umbrella
1913 The potential bias is applied by controlling the position of an harmonic potential
1914 using Monte-Carlo sampling. The force constant is set with
1915 :mdp:`awh1-dim1-force-constant`. The umbrella location
1916 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1917 There are no advantages to using an umbrella.
1918 This option is mainly for comparison and testing purposes.
1920 .. mdp:: awh-share-multisim
1924 AWH will not share biases across simulations started with
1925 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1929 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1930 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1931 with the biases with the same :mdp:`awh1-share-group` value.
1932 The simulations should have the same AWH settings for sharing to make sense.
1933 :ref:`gmx mdrun` will check whether the simulations are technically
1934 compatible for sharing, but the user should check that bias sharing
1935 physically makes sense.
1939 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1940 where -1 indicates to generate a seed. Only used with
1941 :mdp-value:`awh-potential=umbrella`.
1946 Number of steps between printing AWH data to the energy file, should be
1947 a multiple of :mdp:`nstenergy`.
1949 .. mdp:: awh-nstsample
1952 Number of steps between sampling of the coordinate value. This sampling
1953 is the basis for updating the bias and estimating the PMF and other AWH observables.
1955 .. mdp:: awh-nsamples-update
1958 The number of coordinate samples used for each AWH update.
1959 The update interval in steps is :mdp:`awh-nstsample` times this value.
1964 The number of biases, each acting on its own coordinate.
1965 The following options should be specified
1966 for each bias although below only the options for bias number 1 is shown. Options for
1967 other bias indices are obtained by replacing '1' by the bias index.
1969 .. mdp:: awh1-error-init
1971 (10.0) [kJ mol\ :sup:`-1`]
1972 Estimated initial average error of the PMF for this bias. This value together with the
1973 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1974 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1976 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1977 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1978 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1979 then :mdp:`awh1-error-init` should reflect that knowledge.
1981 .. mdp:: awh1-growth
1983 .. mdp-value:: exp-linear
1985 Each bias keeps a reference weight histogram for the coordinate samples.
1986 Its size sets the magnitude of the bias function and free energy estimate updates
1987 (few samples corresponds to large updates and vice versa).
1988 Thus, its growth rate sets the maximum convergence rate.
1989 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1990 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1991 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1992 high free energy barriers have not yet been flattened by the bias.
1994 .. mdp-value:: linear
1996 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1997 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
1998 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
2000 .. mdp:: awh1-equilibrate-histogram
2004 Do not equilibrate histogram.
2008 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
2009 histogram of sampled weights is following the target distribution closely enough (specifically,
2010 at least 80% of the target region needs to have a local relative error of less than 20%). This
2011 option would typically only be used when :mdp:`awh1-share-group` > 0
2012 and the initial configurations poorly represent the target
2015 .. mdp:: awh1-target
2017 .. mdp-value:: constant
2019 The bias is tuned towards a constant (uniform) coordinate distribution
2020 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
2022 .. mdp-value:: cutoff
2024 Similar to :mdp-value:`awh1-target=constant`, but the target
2025 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
2026 where F is the free energy relative to the estimated global minimum.
2027 This provides a smooth switch of a flat target distribution in
2028 regions with free energy lower than the cut-off to a Boltzmann
2029 distribution in regions with free energy higher than the cut-off.
2031 .. mdp-value:: boltzmann
2033 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
2034 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
2035 would give the same coordinate distribution as sampling with a simulation temperature
2038 .. mdp-value:: local-boltzmann
2040 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
2041 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
2042 change of the bias only depends on the local sampling. This local convergence property is
2043 only compatible with :mdp-value:`awh1-growth=linear`, since for
2044 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
2046 .. mdp:: awh1-target-beta-scaling
2049 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
2050 it is the unitless beta scaling factor taking values in (0,1).
2052 .. mdp:: awh1-target-cutoff
2054 (0) [kJ mol\ :sup:`-1`]
2055 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2057 .. mdp:: awh1-user-data
2061 Initialize the PMF and target distribution with default values.
2065 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2066 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2067 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2068 The file name can be changed with the ``-awh`` option.
2069 The first :mdp:`awh1-ndim` columns of
2070 each input file should contain the coordinate values, such that each row defines a point in
2071 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
2072 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2073 be in the same column as written by :ref:`gmx awh`.
2075 .. mdp:: awh1-share-group
2079 Do not share the bias.
2081 .. mdp-value:: positive
2083 Share the bias and PMF estimates within and/or between simulations.
2084 Within a simulation, the bias will be shared between biases that have the
2085 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2086 With :mdp-value:`awh-share-multisim=yes` and
2087 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2088 Sharing may increase convergence initially, although the starting configurations
2089 can be critical, especially when sharing between many biases.
2090 Currently, positive group values should start at 1 and increase
2091 by 1 for each subsequent bias that is shared.
2096 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2097 The following options should be specified for each such dimension. Below only
2098 the options for dimension number 1 is shown. Options for other dimension indices are
2099 obtained by replacing '1' by the dimension index.
2101 .. mdp:: awh1-dim1-coord-provider
2105 The module providing the reaction coordinate for this dimension.
2106 Currently AWH can only act on pull coordinates.
2108 .. mdp:: awh1-dim1-coord-index
2111 Index of the pull coordinate defining this coordinate dimension.
2113 .. mdp:: awh1-dim1-force-constant
2115 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2116 Force constant for the (convolved) umbrella potential(s) along this
2117 coordinate dimension.
2119 .. mdp:: awh1-dim1-start
2122 Start value of the sampling interval along this dimension. The range of allowed
2123 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2124 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2125 is allowed. The interval will then wrap around from +period/2 to -period/2.
2126 For the direction geometry, the dimension is made periodic when
2127 the direction is along a box vector and covers more than 95%
2128 of the box length. Note that one should not apply pressure coupling
2129 along a periodic dimension.
2131 .. mdp:: awh1-dim1-end
2134 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2136 .. mdp:: awh1-dim1-diffusion
2138 (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps]
2139 Estimated diffusion constant for this coordinate dimension determining the initial
2140 biasing rate. This needs only be a rough estimate and should not critically
2141 affect the results unless it is set to something very low, leading to slow convergence,
2142 or very high, forcing the system far from equilibrium. Not setting this value
2143 explicitly generates a warning.
2145 .. mdp:: awh1-dim1-cover-diameter
2148 Diameter that needs to be sampled by a single simulation around a coordinate value
2149 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2150 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2151 across each coordinate value.
2152 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2153 (:mdp:`awh1-share-group`>0).
2154 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2155 for many sharing simulations does not guarantee transitions across free energy barriers.
2156 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2157 has independently sampled the whole interval.
2162 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2163 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2164 that can be used to achieve such a rotation.
2170 No enforced rotation will be applied. All enforced rotation options will
2171 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2176 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2177 under the :mdp:`rot-group0` option.
2179 .. mdp:: rot-ngroups
2182 Number of rotation groups.
2186 Name of rotation group 0 in the index file.
2191 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2192 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2193 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2198 Use mass weighted rotation group positions.
2203 Rotation vector, will get normalized.
2208 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2212 (0) [degree ps\ :sup:`-1`]
2213 Reference rotation rate of group 0.
2217 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2218 Force constant for group 0.
2220 .. mdp:: rot-slab-dist0
2223 Slab distance, if a flexible axis rotation type was chosen.
2225 .. mdp:: rot-min-gauss0
2228 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2229 (for the flexible axis potentials).
2233 (0.0001) [nm\ :sup:`2`]
2234 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2236 .. mdp:: rot-fit-method0
2239 Fitting method when determining the actual angle of a rotation group
2240 (can be one of ``rmsd``, ``norm``, or ``potential``).
2242 .. mdp:: rot-potfit-nsteps0
2245 For fit type ``potential``, the number of angular positions around the reference angle for which the
2246 rotation potential is evaluated.
2248 .. mdp:: rot-potfit-step0
2251 For fit type ``potential``, the distance in degrees between two angular positions.
2253 .. mdp:: rot-nstrout
2256 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2257 and the rotation potential energy.
2259 .. mdp:: rot-nstsout
2262 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2272 ignore distance restraint information in topology file
2274 .. mdp-value:: simple
2276 simple (per-molecule) distance restraints.
2278 .. mdp-value:: ensemble
2280 distance restraints over an ensemble of molecules in one
2281 simulation box. Normally, one would perform ensemble averaging
2282 over multiple simulations, using ``mdrun
2283 -multidir``. The environment
2284 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2285 within each ensemble (usually equal to the number of directories
2286 supplied to ``mdrun -multidir``).
2288 .. mdp:: disre-weighting
2290 .. mdp-value:: equal
2292 divide the restraint force equally over all atom pairs in the
2295 .. mdp-value:: conservative
2297 the forces are the derivative of the restraint potential, this
2298 results in an weighting of the atom pairs to the reciprocal
2299 seventh power of the displacement. The forces are conservative
2300 when :mdp:`disre-tau` is zero.
2302 .. mdp:: disre-mixed
2306 the violation used in the calculation of the restraint force is
2307 the time-averaged violation
2311 the violation used in the calculation of the restraint force is
2312 the square root of the product of the time-averaged violation
2313 and the instantaneous violation
2317 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2318 force constant for distance restraints, which is multiplied by a
2319 (possibly) different factor for each restraint given in the `fac`
2320 column of the interaction in the topology file.
2325 time constant for distance restraints running average. A value of
2326 zero turns off time averaging.
2328 .. mdp:: nstdisreout
2331 period between steps when the running time-averaged and
2332 instantaneous distances of all atom pairs involved in restraints
2333 are written to the energy file (can make the energy file very
2340 ignore orientation restraint information in topology file
2344 use orientation restraints, ensemble averaging can be performed
2345 with ``mdrun -multidir``
2349 (0) [kJ mol\ :sup:`-1`]
2350 force constant for orientation restraints, which is multiplied by a
2351 (possibly) different weight factor for each restraint, can be set
2352 to zero to obtain the orientations from a free simulation
2357 time constant for orientation restraints running average. A value
2358 of zero turns off time averaging.
2360 .. mdp:: orire-fitgrp
2362 fit group for orientation restraining. This group of atoms is used
2363 to determine the rotation **R** of the system with respect to the
2364 reference orientation. The reference orientation is the starting
2365 conformation of the first subsystem. For a protein, backbone is a
2368 .. mdp:: nstorireout
2371 period between steps when the running time-averaged and
2372 instantaneous orientations for all restraints, and the molecular
2373 order tensor are written to the energy file (can make the energy
2377 Free energy calculations
2378 ^^^^^^^^^^^^^^^^^^^^^^^^
2380 .. mdp:: free-energy
2384 Only use topology A.
2388 Interpolate between topology A (lambda=0) to topology B
2389 (lambda=1) and write the derivative of the Hamiltonian with
2390 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2391 or the Hamiltonian differences with respect to other lambda
2392 values (as specified with foreign lambda) to the energy file
2393 and/or to ``dhdl.xvg``, where they can be processed by, for
2394 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2395 are interpolated linearly as described in the manual. When
2396 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2397 used for the LJ and Coulomb interactions.
2401 Turns on expanded ensemble simulation, where the alchemical state
2402 becomes a dynamic variable, allowing jumping between different
2403 Hamiltonians. See the expanded ensemble options for controlling how
2404 expanded ensemble simulations are performed. The different
2405 Hamiltonians used in expanded ensemble simulations are defined by
2406 the other free energy options.
2408 .. mdp:: init-lambda
2411 starting value for lambda (float). Generally, this should only be
2412 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2413 other cases, :mdp:`init-lambda-state` should be specified
2414 instead. Must be greater than or equal to 0.
2416 .. mdp:: delta-lambda
2419 increment per time step for lambda
2421 .. mdp:: init-lambda-state
2424 starting value for the lambda state (integer). Specifies which
2425 columm of the lambda vector (:mdp:`coul-lambdas`,
2426 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2427 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2428 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2429 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2430 the first column, and so on.
2432 .. mdp:: fep-lambdas
2435 Zero, one or more lambda values for which Delta H values will be
2436 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2437 steps. Values must be between 0 and 1. Free energy differences
2438 between different lambda values can then be determined with
2439 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2440 other -lambdas keywords because all components of the lambda vector
2441 that are not specified will use :mdp:`fep-lambdas` (including
2442 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2444 .. mdp:: coul-lambdas
2447 Zero, one or more lambda values for which Delta H values will be
2448 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2449 steps. Values must be between 0 and 1. Only the electrostatic
2450 interactions are controlled with this component of the lambda
2451 vector (and only if the lambda=0 and lambda=1 states have differing
2452 electrostatic interactions).
2454 .. mdp:: vdw-lambdas
2457 Zero, one or more lambda values for which Delta H values will be
2458 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2459 steps. Values must be between 0 and 1. Only the van der Waals
2460 interactions are controlled with this component of the lambda
2463 .. mdp:: bonded-lambdas
2466 Zero, one or more lambda values for which Delta H values will be
2467 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2468 steps. Values must be between 0 and 1. Only the bonded interactions
2469 are controlled with this component of the lambda vector.
2471 .. mdp:: restraint-lambdas
2474 Zero, one or more lambda values for which Delta H values will be
2475 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2476 steps. Values must be between 0 and 1. Only the restraint
2477 interactions: dihedral restraints, and the pull code restraints are
2478 controlled with this component of the lambda vector.
2480 .. mdp:: mass-lambdas
2483 Zero, one or more lambda values for which Delta H values will be
2484 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2485 steps. Values must be between 0 and 1. Only the particle masses are
2486 controlled with this component of the lambda vector.
2488 .. mdp:: temperature-lambdas
2491 Zero, one or more lambda values for which Delta H values will be
2492 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2493 steps. Values must be between 0 and 1. Only the temperatures
2494 controlled with this component of the lambda vector. Note that
2495 these lambdas should not be used for replica exchange, only for
2496 simulated tempering.
2498 .. mdp:: calc-lambda-neighbors
2501 Controls the number of lambda values for which Delta H values will
2502 be calculated and written out, if :mdp:`init-lambda-state` has
2503 been set. A positive value will limit the number of lambda points
2504 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2505 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2506 has a value of 2, energies for lambda points 3-7 will be calculated
2507 and writen out. A value of -1 means all lambda points will be
2508 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2509 1 is sufficient, while for MBAR -1 should be used.
2514 the soft-core alpha parameter, a value of 0 results in linear
2515 interpolation of the LJ and Coulomb interactions
2520 the power of the radial term in the soft-core equation. Possible
2521 values are 6 and 48. 6 is more standard, and is the default. When
2522 48 is used, then sc-alpha should generally be much lower (between
2528 Whether to apply the soft-core free energy interaction
2529 transformation to the Columbic interaction of a molecule. Default
2530 is no, as it is generally more efficient to turn off the Coulomic
2531 interactions linearly before turning off the van der Waals
2532 interactions. Note that it is only taken into account when lambda
2533 states are used, not with :mdp:`couple-lambda0` /
2534 :mdp:`couple-lambda1`, and you can still turn off soft-core
2535 interactions by setting :mdp:`sc-alpha` to 0.
2540 the power for lambda in the soft-core function, only the values 1
2546 the soft-core sigma for particles which have a C6 or C12 parameter
2547 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2549 .. mdp:: couple-moltype
2551 Here one can supply a molecule type (as defined in the topology)
2552 for calculating solvation or coupling free energies. There is a
2553 special option ``system`` that couples all molecule types in the
2554 system. This can be useful for equilibrating a system starting from
2555 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2556 on. The Van der Waals interactions and/or charges in this molecule
2557 type can be turned on or off between lambda=0 and lambda=1,
2558 depending on the settings of :mdp:`couple-lambda0` and
2559 :mdp:`couple-lambda1`. If you want to decouple one of several
2560 copies of a molecule, you need to copy and rename the molecule
2561 definition in the topology.
2563 .. mdp:: couple-lambda0
2565 .. mdp-value:: vdw-q
2567 all interactions are on at lambda=0
2571 the charges are zero (no Coulomb interactions) at lambda=0
2575 the Van der Waals interactions are turned at lambda=0; soft-core
2576 interactions will be required to avoid singularities
2580 the Van der Waals interactions are turned off and the charges
2581 are zero at lambda=0; soft-core interactions will be required to
2582 avoid singularities.
2584 .. mdp:: couple-lambda1
2586 analogous to :mdp:`couple-lambda1`, but for lambda=1
2588 .. mdp:: couple-intramol
2592 All intra-molecular non-bonded interactions for moleculetype
2593 :mdp:`couple-moltype` are replaced by exclusions and explicit
2594 pair interactions. In this manner the decoupled state of the
2595 molecule corresponds to the proper vacuum state without
2596 periodicity effects.
2600 The intra-molecular Van der Waals and Coulomb interactions are
2601 also turned on/off. This can be useful for partitioning
2602 free-energies of relatively large molecules, where the
2603 intra-molecular non-bonded interactions might lead to
2604 kinetically trapped vacuum conformations. The 1-4 pair
2605 interactions are not turned off.
2610 the frequency for writing dH/dlambda and possibly Delta H to
2611 dhdl.xvg, 0 means no ouput, should be a multiple of
2612 :mdp:`nstcalcenergy`.
2614 .. mdp:: dhdl-derivatives
2618 If yes (the default), the derivatives of the Hamiltonian with
2619 respect to lambda at each :mdp:`nstdhdl` step are written
2620 out. These values are needed for interpolation of linear energy
2621 differences with :ref:`gmx bar` (although the same can also be
2622 achieved with the right foreign lambda setting, that may not be as
2623 flexible), or with thermodynamic integration
2625 .. mdp:: dhdl-print-energy
2629 Include either the total or the potential energy in the dhdl
2630 file. Options are 'no', 'potential', or 'total'. This information
2631 is needed for later free energy analysis if the states of interest
2632 are at different temperatures. If all states are at the same
2633 temperature, this information is not needed. 'potential' is useful
2634 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2635 file. When rerunning from an existing trajectory, the kinetic
2636 energy will often not be correct, and thus one must compute the
2637 residual free energy from the potential alone, with the kinetic
2638 energy component computed analytically.
2640 .. mdp:: separate-dhdl-file
2644 The free energy values that are calculated (as specified with
2645 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2646 written out to a separate file, with the default name
2647 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2652 The free energy values are written out to the energy output file
2653 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2654 steps), where they can be extracted with :ref:`gmx energy` or
2655 used directly with :ref:`gmx bar`.
2657 .. mdp:: dh-hist-size
2660 If nonzero, specifies the size of the histogram into which the
2661 Delta H values (specified with foreign lambda) and the derivative
2662 dH/dl values are binned, and written to ener.edr. This can be used
2663 to save disk space while calculating free energy differences. One
2664 histogram gets written for each foreign lambda and two for the
2665 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2666 histogram settings (too small size or too wide bins) can introduce
2667 errors. Do not use histograms unless you're certain you need it.
2669 .. mdp:: dh-hist-spacing
2672 Specifies the bin width of the histograms, in energy units. Used in
2673 conjunction with :mdp:`dh-hist-size`. This size limits the
2674 accuracy with which free energies can be calculated. Do not use
2675 histograms unless you're certain you need it.
2678 Expanded Ensemble calculations
2679 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2681 .. mdp:: nstexpanded
2683 The number of integration steps beween attempted moves changing the
2684 system Hamiltonian in expanded ensemble simulations. Must be a
2685 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2692 No Monte Carlo in state space is performed.
2694 .. mdp-value:: metropolis-transition
2696 Uses the Metropolis weights to update the expanded ensemble
2697 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2700 .. mdp-value:: barker-transition
2702 Uses the Barker transition critera to update the expanded
2703 ensemble weight of each state i, defined by exp(-beta_new
2704 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2706 .. mdp-value:: wang-landau
2708 Uses the Wang-Landau algorithm (in state space, not energy
2709 space) to update the expanded ensemble weights.
2711 .. mdp-value:: min-variance
2713 Uses the minimum variance updating method of Escobedo et al. to
2714 update the expanded ensemble weights. Weights will not be the
2715 free energies, but will rather emphasize states that need more
2716 sampling to give even uncertainty.
2718 .. mdp:: lmc-mc-move
2722 No Monte Carlo in state space is performed.
2724 .. mdp-value:: metropolis-transition
2726 Randomly chooses a new state up or down, then uses the
2727 Metropolis critera to decide whether to accept or reject:
2728 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2730 .. mdp-value:: barker-transition
2732 Randomly chooses a new state up or down, then uses the Barker
2733 transition critera to decide whether to accept or reject:
2734 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2736 .. mdp-value:: gibbs
2738 Uses the conditional weights of the state given the coordinate
2739 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2742 .. mdp-value:: metropolized-gibbs
2744 Uses the conditional weights of the state given the coordinate
2745 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2746 to move to, EXCLUDING the current state, then uses a rejection
2747 step to ensure detailed balance. Always more efficient that
2748 Gibbs, though only marginally so in many situations, such as
2749 when only the nearest neighbors have decent phase space
2755 random seed to use for Monte Carlo moves in state space. When
2756 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2758 .. mdp:: mc-temperature
2760 Temperature used for acceptance/rejection for Monte Carlo moves. If
2761 not specified, the temperature of the simulation specified in the
2762 first group of :mdp:`ref-t` is used.
2767 The cutoff for the histogram of state occupancies to be reset, and
2768 the free energy incrementor to be changed from delta to delta *
2769 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2770 each histogram) / (average number of samples at each
2771 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2772 histogram is only considered flat if all Nratio > 0.8 AND
2773 simultaneously all 1/Nratio > 0.8.
2778 Each time the histogram is considered flat, then the current value
2779 of the Wang-Landau incrementor for the free energies is multiplied
2780 by :mdp:`wl-scale`. Value must be between 0 and 1.
2782 .. mdp:: init-wl-delta
2785 The initial value of the Wang-Landau incrementor in kT. Some value
2786 near 1 kT is usually most efficient, though sometimes a value of
2787 2-3 in units of kT works better if the free energy differences are
2790 .. mdp:: wl-oneovert
2793 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2794 the large sample limit. There is significant evidence that the
2795 standard Wang-Landau algorithms in state space presented here
2796 result in free energies getting 'burned in' to incorrect values
2797 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2798 then when the incrementor becomes less than 1/N, where N is the
2799 mumber of samples collected (and thus proportional to the data
2800 collection time, hence '1 over t'), then the Wang-Lambda
2801 incrementor is set to 1/N, decreasing every step. Once this occurs,
2802 :mdp:`wl-ratio` is ignored, but the weights will still stop
2803 updating when the equilibration criteria set in
2804 :mdp:`lmc-weights-equil` is achieved.
2806 .. mdp:: lmc-repeats
2809 Controls the number of times that each Monte Carlo swap type is
2810 performed each iteration. In the limit of large numbers of Monte
2811 Carlo repeats, then all methods converge to Gibbs sampling. The
2812 value will generally not need to be different from 1.
2814 .. mdp:: lmc-gibbsdelta
2817 Limit Gibbs sampling to selected numbers of neighboring states. For
2818 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2819 sampling over all of the states that are defined. A positive value
2820 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2821 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2822 value of -1 means that all states are considered. For less than 100
2823 states, it is probably not that expensive to include all states.
2825 .. mdp:: lmc-forced-nstart
2828 Force initial state space sampling to generate weights. In order to
2829 come up with reasonable initial weights, this setting allows the
2830 simulation to drive from the initial to the final lambda state,
2831 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2832 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2833 sufficiently long (thousands of steps, perhaps), then the weights
2834 will be close to correct. However, in most cases, it is probably
2835 better to simply run the standard weight equilibration algorithms.
2837 .. mdp:: nst-transition-matrix
2840 Frequency of outputting the expanded ensemble transition matrix. A
2841 negative number means it will only be printed at the end of the
2844 .. mdp:: symmetrized-transition-matrix
2847 Whether to symmetrize the empirical transition matrix. In the
2848 infinite limit the matrix will be symmetric, but will diverge with
2849 statistical noise for short timescales. Forced symmetrization, by
2850 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2851 like the existence of (small magnitude) negative eigenvalues.
2853 .. mdp:: mininum-var-min
2856 The min-variance strategy (option of :mdp:`lmc-stats` is only
2857 valid for larger number of samples, and can get stuck if too few
2858 samples are used at each state. :mdp:`mininum-var-min` is the
2859 minimum number of samples that each state that are allowed before
2860 the min-variance strategy is activated if selected.
2862 .. mdp:: init-lambda-weights
2864 The initial weights (free energies) used for the expanded ensemble
2865 states. Default is a vector of zero weights. format is similar to
2866 the lambda vector settings in :mdp:`fep-lambdas`, except the
2867 weights can be any floating point number. Units are kT. Its length
2868 must match the lambda vector lengths.
2870 .. mdp:: lmc-weights-equil
2874 Expanded ensemble weights continue to be updated throughout the
2879 The input expanded ensemble weights are treated as equilibrated,
2880 and are not updated throughout the simulation.
2882 .. mdp-value:: wl-delta
2884 Expanded ensemble weight updating is stopped when the
2885 Wang-Landau incrementor falls below this value.
2887 .. mdp-value:: number-all-lambda
2889 Expanded ensemble weight updating is stopped when the number of
2890 samples at all of the lambda states is greater than this value.
2892 .. mdp-value:: number-steps
2894 Expanded ensemble weight updating is stopped when the number of
2895 steps is greater than the level specified by this value.
2897 .. mdp-value:: number-samples
2899 Expanded ensemble weight updating is stopped when the number of
2900 total samples across all lambda states is greater than the level
2901 specified by this value.
2903 .. mdp-value:: count-ratio
2905 Expanded ensemble weight updating is stopped when the ratio of
2906 samples at the least sampled lambda state and most sampled
2907 lambda state greater than this value.
2909 .. mdp:: simulated-tempering
2912 Turn simulated tempering on or off. Simulated tempering is
2913 implemented as expanded ensemble sampling with different
2914 temperatures instead of different Hamiltonians.
2916 .. mdp:: sim-temp-low
2919 Low temperature for simulated tempering.
2921 .. mdp:: sim-temp-high
2924 High temperature for simulated tempering.
2926 .. mdp:: simulated-tempering-scaling
2928 Controls the way that the temperatures at intermediate lambdas are
2929 calculated from the :mdp:`temperature-lambdas` part of the lambda
2932 .. mdp-value:: linear
2934 Linearly interpolates the temperatures using the values of
2935 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2936 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2937 a temperature of 350. A nonlinear set of temperatures can always
2938 be implemented with uneven spacing in lambda.
2940 .. mdp-value:: geometric
2942 Interpolates temperatures geometrically between
2943 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2944 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2945 :mdp:`sim-temp-low`) raised to the power of
2946 (i/(ntemps-1)). This should give roughly equal exchange for
2947 constant heat capacity, though of course things simulations that
2948 involve protein folding have very high heat capacity peaks.
2950 .. mdp-value:: exponential
2952 Interpolates temperatures exponentially between
2953 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2954 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2955 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2956 (i))-1)/(exp(1.0)-i)).
2964 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2965 in groups Protein and Sol will experience constant acceleration as
2966 specified in the :mdp:`accelerate` line
2970 (0) [nm ps\ :sup:`-2`]
2971 acceleration for :mdp:`acc-grps`; x, y and z for each group
2972 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2973 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
2978 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2979 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2980 specifies for which dimension(s) the freezing applies. To avoid
2981 spurious contributions to the virial and pressure due to large
2982 forces between completely frozen atoms you need to use energy group
2983 exclusions, this also saves computing time. Note that coordinates
2984 of frozen atoms are not scaled by pressure-coupling algorithms.
2988 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2989 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
2990 N N N N`` means that particles in the first group can move only in
2991 Z direction. The particles in the second group can move in any
2994 .. mdp:: cos-acceleration
2996 (0) [nm ps\ :sup:`-2`]
2997 the amplitude of the acceleration profile for calculating the
2998 viscosity. The acceleration is in the X-direction and the magnitude
2999 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
3000 added to the energy file: the amplitude of the velocity profile and
3005 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
3006 The velocities of deformation for the box elements: a(x) b(y) c(z)
3007 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
3008 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
3009 elements are corrected for periodicity. The coordinates are
3010 transformed accordingly. Frozen degrees of freedom are (purposely)
3011 also transformed. The time ts is set to t at the first step and at
3012 steps at which x and v are written to trajectory to ensure exact
3013 restarts. Deformation can be used together with semiisotropic or
3014 anisotropic pressure coupling when the appropriate
3015 compressibilities are set to zero. The diagonal elements can be
3016 used to strain a solid. The off-diagonal elements can be used to
3017 shear a solid or a liquid.
3023 .. mdp:: electric-field-x
3024 .. mdp:: electric-field-y
3025 .. mdp:: electric-field-z
3027 Here you can specify an electric field that optionally can be
3028 alternating and pulsed. The general expression for the field
3029 has the form of a gaussian laser pulse:
3031 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
3033 For example, the four parameters for direction x are set in the
3034 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
3035 and ``electric-field-z``) like
3037 ``electric-field-x = E0 omega t0 sigma``
3039 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
3041 In the special case that ``sigma = 0``, the exponential term is omitted
3042 and only the cosine term is used. If also ``omega = 0`` a static
3043 electric field is applied.
3045 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
3048 Mixed quantum/classical molecular dynamics
3049 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3059 Do a QM/MM simulation. Several groups can be described at
3060 different QM levels separately. These are specified in the
3061 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
3062 initio* theory at which the groups are described is specified by
3063 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
3064 groups at different levels of theory is only possible with the
3065 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
3069 groups to be descibed at the QM level (works also in case of MiMiC QM/MM)
3073 .. mdp-value:: normal
3075 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
3076 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
3077 *ab initio* theory. The rest of the system is described at the
3078 MM level. The QM and MM subsystems interact as follows: MM point
3079 charges are included in the QM one-electron hamiltonian and all
3080 Lennard-Jones interactions are described at the MM level.
3082 .. mdp-value:: ONIOM
3084 The interaction between the subsystem is described using the
3085 ONIOM method by Morokuma and co-workers. There can be more than
3086 one :mdp:`QMMM-grps` each modeled at a different level of QM
3087 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
3092 Method used to compute the energy and gradients on the QM
3093 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
3094 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
3095 included in the active space is specified by :mdp:`CASelectrons`
3096 and :mdp:`CASorbitals`.
3101 Basis set used to expand the electronic wavefuntion. Only Gaussian
3102 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3103 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
3108 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
3109 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
3110 layer needs to be specified separately.
3115 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
3116 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
3117 needs to be specified separately.
3119 .. mdp:: CASorbitals
3122 The number of orbitals to be included in the active space when
3123 doing a CASSCF computation.
3125 .. mdp:: CASelectrons
3128 The number of electrons to be included in the active space when
3129 doing a CASSCF computation.
3135 No surface hopping. The system is always in the electronic
3140 Do a QM/MM MD simulation on the excited state-potential energy
3141 surface and enforce a *diabatic* hop to the ground-state when
3142 the system hits the conical intersection hyperline in the course
3143 the simulation. This option only works in combination with the
3147 Computational Electrophysiology
3148 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3149 Use these options to switch on and control ion/water position exchanges in "Computational
3150 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3156 Do not enable ion/water position exchanges.
3158 .. mdp-value:: X ; Y ; Z
3160 Allow for ion/water position exchanges along the chosen direction.
3161 In a typical setup with the membranes parallel to the x-y plane,
3162 ion/water pairs need to be exchanged in Z direction to sustain the
3163 requested ion concentrations in the compartments.
3165 .. mdp:: swap-frequency
3167 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3168 per compartment are determined and exchanges made if necessary.
3169 Normally it is not necessary to check at every time step.
3170 For typical Computational Electrophysiology setups, a value of about 100 is
3171 sufficient and yields a negligible performance impact.
3173 .. mdp:: split-group0
3175 Name of the index group of the membrane-embedded part of channel #0.
3176 The center of mass of these atoms defines one of the compartment boundaries
3177 and should be chosen such that it is near the center of the membrane.
3179 .. mdp:: split-group1
3181 Channel #1 defines the position of the other compartment boundary.
3183 .. mdp:: massw-split0
3185 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3189 Use the geometrical center.
3193 Use the center of mass.
3195 .. mdp:: massw-split1
3197 (no) As above, but for split-group #1.
3199 .. mdp:: solvent-group
3201 Name of the index group of solvent molecules.
3203 .. mdp:: coupl-steps
3205 (10) Average the number of ions per compartment over these many swap attempt steps.
3206 This can be used to prevent that ions near a compartment boundary
3207 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3211 (1) The number of different ion types to be controlled. These are during the
3212 simulation exchanged with solvent molecules to reach the desired reference numbers.
3214 .. mdp:: iontype0-name
3216 Name of the first ion type.
3218 .. mdp:: iontype0-in-A
3220 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3221 The default value of -1 means: use the number of ions as found in time step 0
3224 .. mdp:: iontype0-in-B
3226 (-1) Reference number of ions of type 0 for compartment B.
3228 .. mdp:: bulk-offsetA
3230 (0.0) Offset of the first swap layer from the compartment A midplane.
3231 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3232 at maximum distance (= bulk concentration) to the split group layers. However,
3233 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3234 towards one of the compartment-partitioning layers (at +/- 1.0).
3236 .. mdp:: bulk-offsetB
3238 (0.0) Offset of the other swap layer from the compartment B midplane.
3243 (\1) Only swap ions if threshold difference to requested count is reached.
3247 (2.0) [nm] Radius of the split cylinder #0.
3248 Two split cylinders (mimicking the channel pores) can optionally be defined
3249 relative to the center of the split group. With the help of these cylinders
3250 it can be counted which ions have passed which channel. The split cylinder
3251 definition has no impact on whether or not ion/water swaps are done.
3255 (1.0) [nm] Upper extension of the split cylinder #0.
3259 (1.0) [nm] Lower extension of the split cylinder #0.
3263 (2.0) [nm] Radius of the split cylinder #1.
3267 (1.0) [nm] Upper extension of the split cylinder #1.
3271 (1.0) [nm] Lower extension of the split cylinder #1.
3274 User defined thingies
3275 ^^^^^^^^^^^^^^^^^^^^^
3279 .. mdp:: userint1 (0)
3280 .. mdp:: userint2 (0)
3281 .. mdp:: userint3 (0)
3282 .. mdp:: userint4 (0)
3283 .. mdp:: userreal1 (0)
3284 .. mdp:: userreal2 (0)
3285 .. mdp:: userreal3 (0)
3286 .. mdp:: userreal4 (0)
3288 These you can use if you modify code. You can pass integers and
3289 reals and groups to your subroutine. Check the inputrec definition
3290 in ``src/gromacs/mdtypes/inputrec.h``
3295 These features have been removed from |Gromacs|, but so that old
3296 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3297 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3298 fatal error if this is set.
3304 .. mdp:: implicit-solvent
3308 .. _reference manual: gmx-manual-parent-dir_