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:: Generalized-Reaction-Field
627 Generalized reaction field with Coulomb cut-off
628 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rcoulomb`. The
629 dielectric constant beyond the cut-off is
630 :mdp:`epsilon-rf`. The ionic strength is computed from the
631 number of charged (*i.e.* with non zero charge) charge
632 groups. The temperature for the GRF potential is set with
635 .. mdp-value:: Reaction-Field-zero
637 In |Gromacs|, normal reaction-field electrostatics with
638 :mdp-value:`cutoff-scheme=group` leads to bad energy
639 conservation. :mdp-value:`coulombtype=Reaction-Field-zero` solves this by making
640 the potential zero beyond the cut-off. It can only be used with
641 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
642 only for that value the force vanishes at the
643 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
644 :mdp:`rcoulomb` to accommodate the size of charge groups
645 and diffusion between neighbor list updates. This, and the fact
646 that table lookups are used instead of analytical functions make
647 reaction-field-zero computationally more expensive than
648 normal reaction-field.
652 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
653 might want to use :mdp-value:`coulombtype=Reaction-Field-zero` instead, which has
654 a similar potential shape, but has a physical interpretation and
655 has better energies due to the exclusion correction terms.
657 .. mdp-value:: Encad-Shift
659 The Coulomb potential is decreased over the whole range, using
660 the definition from the Encad simulation package.
662 .. mdp-value:: Switch
664 Analogous to :mdp-value:`vdwtype=Switch` for
665 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
666 serious artifacts, advice: use :mdp-value:`coulombtype=Reaction-Field-zero`
671 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
672 with user-defined potential functions for repulsion, dispersion
673 and Coulomb. When pair interactions are present, :ref:`gmx
674 mdrun` also expects to find a file ``tablep.xvg`` for the pair
675 interactions. When the same interactions should be used for
676 non-bonded and pair interactions the user can specify the same
677 file name for both table files. These files should contain 7
678 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
679 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
680 function, ``g(x)`` the dispersion function and ``h(x)`` the
681 repulsion function. When :mdp:`vdwtype` is not set to User the
682 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
683 the non-bonded interactions ``x`` values should run from 0 to
684 the largest cut-off distance + :mdp:`table-extension` and
685 should be uniformly spaced. For the pair interactions the table
686 length in the file will be used. The optimal spacing, which is
687 used for non-user tables, is ``0.002 nm`` when you run in mixed
688 precision or ``0.0005 nm`` when you run in double precision. The
689 function value at ``x=0`` is not important. More information is
690 in the printed manual.
692 .. mdp-value:: PME-Switch
694 A combination of PME and a switch function for the direct-space
695 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
696 :mdp:`rlist`. This is mainly useful constant energy simulations
697 (note that using PME with :mdp-value:`cutoff-scheme=Verlet`
698 will be more efficient).
700 .. mdp-value:: PME-User
702 A combination of PME and user tables (see
703 above). :mdp:`rcoulomb` is allowed to be smaller than
704 :mdp:`rlist`. The PME mesh contribution is subtracted from the
705 user table by :ref:`gmx mdrun`. Because of this subtraction the
706 user tables should contain about 10 decimal places.
708 .. mdp-value:: PME-User-Switch
710 A combination of PME-User and a switching function (see
711 above). The switching function is applied to final
712 particle-particle interaction, *i.e.* both to the user supplied
713 function and the PME Mesh correction part.
715 .. mdp:: coulomb-modifier
717 .. mdp-value:: Potential-shift-Verlet
719 Selects Potential-shift with the Verlet cutoff-scheme, as it is
720 (nearly) free; selects None with the group cutoff-scheme.
722 .. mdp-value:: Potential-shift
724 Shift the Coulomb potential by a constant such that it is zero
725 at the cut-off. This makes the potential the integral of the
726 force. Note that this does not affect the forces or the
731 Use an unmodified Coulomb potential. With the group scheme this
732 means no exact cut-off is used, energies and forces are
733 calculated for all pairs in the pair list.
735 .. mdp:: rcoulomb-switch
738 where to start switching the Coulomb potential, only relevant
739 when force or potential switching is used
744 The distance for the Coulomb cut-off. Note that with PME this value
745 can be increased by the PME tuning in :ref:`gmx mdrun` along with
746 the PME grid spacing.
751 The relative dielectric constant. A value of 0 means infinity.
756 The relative dielectric constant of the reaction field. This
757 is only used with reaction-field electrostatics. A value of 0
766 .. mdp-value:: Cut-off
768 Plain cut-off with pair list radius :mdp:`rlist` and VdW
769 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
773 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
774 grid dimensions are controlled with :mdp:`fourierspacing` in
775 the same way as for electrostatics, and the interpolation order
776 is controlled with :mdp:`pme-order`. The relative accuracy of
777 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
778 and the specific combination rules that are to be used by the
779 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
783 This functionality is deprecated and replaced by using
784 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
785 The LJ (not Buckingham) potential is decreased over the whole range and
786 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
787 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
788 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
789 size of charge groups and diffusion between neighbor list
792 .. mdp-value:: Switch
794 This functionality is deprecated and replaced by using
795 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
796 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
797 which it is switched off to reach zero at :mdp:`rvdw`. Both the
798 potential and force functions are continuously smooth, but be
799 aware that all switch functions will give rise to a bulge
800 (increase) in the force (since we are switching the
801 potential). The neighbor search cut-off :mdp:`rlist` should be
802 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
803 size of charge groups and diffusion between neighbor list
806 .. mdp-value:: Encad-Shift
808 The LJ (not Buckingham) potential is decreased over the whole
809 range, using the definition from the Encad simulation package.
813 See user for :mdp:`coulombtype`. The function value at zero is
814 not important. When you want to use LJ correction, make sure
815 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
816 function. When :mdp:`coulombtype` is not set to User the values
817 for the ``f`` and ``-f'`` columns are ignored.
819 .. mdp:: vdw-modifier
821 .. mdp-value:: Potential-shift-Verlet
823 Selects Potential-shift with the Verlet cutoff-scheme, as it is
824 (nearly) free; selects None with the group cutoff-scheme.
826 .. mdp-value:: Potential-shift
828 Shift the Van der Waals potential by a constant such that it is
829 zero at the cut-off. This makes the potential the integral of
830 the force. Note that this does not affect the forces or the
835 Use an unmodified Van der Waals potential. With the group scheme
836 this means no exact cut-off is used, energies and forces are
837 calculated for all pairs in the pair list.
839 .. mdp-value:: Force-switch
841 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
842 and :mdp:`rvdw`. This shifts the potential shift over the whole
843 range and switches it to zero at the cut-off. Note that this is
844 more expensive to calculate than a plain cut-off and it is not
845 required for energy conservation, since Potential-shift
846 conserves energy just as well.
848 .. mdp-value:: Potential-switch
850 Smoothly switches the potential to zero between
851 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
852 articifically large forces in the switching region and is much
853 more expensive to calculate. This option should only be used if
854 the force field you are using requires this.
859 where to start switching the LJ force and possibly the potential,
860 only relevant when force or potential switching is used
865 distance for the LJ or Buckingham cut-off
871 don't apply any correction
873 .. mdp-value:: EnerPres
875 apply long range dispersion corrections for Energy and Pressure
879 apply long range dispersion corrections for Energy only
885 .. mdp:: table-extension
888 Extension of the non-bonded potential lookup tables beyond the
889 largest cut-off distance. The value should be large enough to
890 account for charge group sizes and the diffusion between
891 neighbor-list updates. Without user defined potential the same
892 table length is used for the lookup tables for the 1-4
893 interactions, which are always tabulated irrespective of the use of
894 tables for the non-bonded interactions. The value of
895 :mdp:`table-extension` in no way affects the values of
896 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
898 .. mdp:: energygrp-table
900 When user tables are used for electrostatics and/or VdW, here one
901 can give pairs of energy groups for which seperate user tables
902 should be used. The two energy groups will be appended to the table
903 file name, in order of their definition in :mdp:`energygrps`,
904 seperated by underscores. For example, if ``energygrps = Na Cl
905 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
906 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
907 normal ``table.xvg`` which will be used for all other energy group
914 .. mdp:: fourierspacing
917 For ordinary Ewald, the ratio of the box dimensions and the spacing
918 determines a lower bound for the number of wave vectors to use in
919 each (signed) direction. For PME and P3M, that ratio determines a
920 lower bound for the number of Fourier-space grid points that will
921 be used along that axis. In all cases, the number for each
922 direction can be overridden by entering a non-zero value for that
923 :mdp:`fourier-nx` direction. For optimizing the relative load of
924 the particle-particle interactions and the mesh part of PME, it is
925 useful to know that the accuracy of the electrostatics remains
926 nearly constant when the Coulomb cut-off and the PME grid spacing
927 are scaled by the same factor. Note that this spacing can be scaled
928 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
935 Highest magnitude of wave vectors in reciprocal space when using Ewald.
936 Grid size when using PME or P3M. These values override
937 :mdp:`fourierspacing` per direction. The best choice is powers of
938 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
939 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
945 Interpolation order for PME. 4 equals cubic interpolation. You
946 might try 6/8/10 when running in parallel and simultaneously
947 decrease grid dimension.
952 The relative strength of the Ewald-shifted direct potential at
953 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
954 will give a more accurate direct sum, but then you need more wave
955 vectors for the reciprocal sum.
957 .. mdp:: ewald-rtol-lj
960 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
961 to control the relative strength of the dispersion potential at
962 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
963 electrostatic potential.
965 .. mdp:: lj-pme-comb-rule
968 The combination rules used to combine VdW-parameters in the
969 reciprocal part of LJ-PME. Geometric rules are much faster than
970 Lorentz-Berthelot and usually the recommended choice, even when the
971 rest of the force field uses the Lorentz-Berthelot rules.
973 .. mdp-value:: Geometric
975 Apply geometric combination rules
977 .. mdp-value:: Lorentz-Berthelot
979 Apply Lorentz-Berthelot combination rules
981 .. mdp:: ewald-geometry
985 The Ewald sum is performed in all three dimensions.
989 The reciprocal sum is still performed in 3D, but a force and
990 potential correction applied in the `z` dimension to produce a
991 pseudo-2D summation. If your system has a slab geometry in the
992 `x-y` plane you can try to increase the `z`-dimension of the box
993 (a box height of 3 times the slab height is usually ok) and use
996 .. mdp:: epsilon-surface
999 This controls the dipole correction to the Ewald summation in
1000 3D. The default value of zero means it is turned off. Turn it on by
1001 setting it to the value of the relative permittivity of the
1002 imaginary surface around your infinite system. Be careful - you
1003 shouldn't use this if you have free mobile charges in your
1004 system. This value does not affect the slab 3DC variant of the long
1008 Temperature coupling
1009 ^^^^^^^^^^^^^^^^^^^^
1015 No temperature coupling.
1017 .. mdp-value:: berendsen
1019 Temperature coupling with a Berendsen thermostat to a bath with
1020 temperature :mdp:`ref-t`, with time constant
1021 :mdp:`tau-t`. Several groups can be coupled separately, these
1022 are specified in the :mdp:`tc-grps` field separated by spaces.
1024 .. mdp-value:: nose-hoover
1026 Temperature coupling using a Nose-Hoover extended ensemble. The
1027 reference temperature and coupling groups are selected as above,
1028 but in this case :mdp:`tau-t` controls the period of the
1029 temperature fluctuations at equilibrium, which is slightly
1030 different from a relaxation time. For NVT simulations the
1031 conserved energy quantity is written to the energy and log files.
1033 .. mdp-value:: andersen
1035 Temperature coupling by randomizing a fraction of the particle velocities
1036 at each timestep. Reference temperature and coupling groups are
1037 selected as above. :mdp:`tau-t` is the average time between
1038 randomization of each molecule. Inhibits particle dynamics
1039 somewhat, but little or no ergodicity issues. Currently only
1040 implemented with velocity Verlet, and not implemented with
1043 .. mdp-value:: andersen-massive
1045 Temperature coupling by randomizing velocities of all particles at
1046 infrequent timesteps. Reference temperature and coupling groups are
1047 selected as above. :mdp:`tau-t` is the time between
1048 randomization of all molecules. Inhibits particle dynamics
1049 somewhat, but little or no ergodicity issues. Currently only
1050 implemented with velocity Verlet.
1052 .. mdp-value:: v-rescale
1054 Temperature coupling using velocity rescaling with a stochastic
1055 term (JCP 126, 014101). This thermostat is similar to Berendsen
1056 coupling, with the same scaling using :mdp:`tau-t`, but the
1057 stochastic term ensures that a proper canonical ensemble is
1058 generated. The random seed is set with :mdp:`ld-seed`. This
1059 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1060 simulations the conserved energy quantity is written to the
1061 energy and log file.
1066 The frequency for coupling the temperature. The default value of -1
1067 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1068 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1069 Verlet integrators :mdp:`nsttcouple` is set to 1.
1071 .. mdp:: nh-chain-length
1074 The number of chained Nose-Hoover thermostats for velocity Verlet
1075 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1076 only supports 1. Data for the NH chain variables is not printed
1077 to the :ref:`edr` file by default, but can be turned on with the
1078 :mdp:`print-nose-hoover-chain-variables` option.
1080 .. mdp:: print-nose-hoover-chain-variables
1084 Do not store Nose-Hoover chain variables in the energy file.
1088 Store all positions and velocities of the Nose-Hoover chain
1093 groups to couple to separate temperature baths
1098 time constant for coupling (one for each group in
1099 :mdp:`tc-grps`), -1 means no temperature coupling
1104 reference temperature for coupling (one for each group in
1115 No pressure coupling. This means a fixed box size.
1117 .. mdp-value:: Berendsen
1119 Exponential relaxation pressure coupling with time constant
1120 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1121 argued that this does not yield a correct thermodynamic
1122 ensemble, but it is the most efficient way to scale a box at the
1125 .. mdp-value:: Parrinello-Rahman
1127 Extended-ensemble pressure coupling where the box vectors are
1128 subject to an equation of motion. The equation of motion for the
1129 atoms is coupled to this. No instantaneous scaling takes
1130 place. As for Nose-Hoover temperature coupling the time constant
1131 :mdp:`tau-p` is the period of pressure fluctuations at
1132 equilibrium. This is probably a better method when you want to
1133 apply pressure scaling during data collection, but beware that
1134 you can get very large oscillations if you are starting from a
1135 different pressure. For simulations where the exact fluctations
1136 of the NPT ensemble are important, or if the pressure coupling
1137 time is very short it may not be appropriate, as the previous
1138 time step pressure is used in some steps of the |Gromacs|
1139 implementation for the current time step pressure.
1143 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1144 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1145 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1146 time constant :mdp:`tau-p` is the period of pressure
1147 fluctuations at equilibrium. This is probably a better method
1148 when you want to apply pressure scaling during data collection,
1149 but beware that you can get very large oscillations if you are
1150 starting from a different pressure. Currently (as of version
1151 5.1), it only supports isotropic scaling, and only works without
1156 Specifies the kind of isotropy of the pressure coupling used. Each
1157 kind takes one or more values for :mdp:`compressibility` and
1158 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1160 .. mdp-value:: isotropic
1162 Isotropic pressure coupling with time constant
1163 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1164 :mdp:`ref-p` is required.
1166 .. mdp-value:: semiisotropic
1168 Pressure coupling which is isotropic in the ``x`` and ``y``
1169 direction, but different in the ``z`` direction. This can be
1170 useful for membrane simulations. Two values each for
1171 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1172 ``x/y`` and ``z`` directions respectively.
1174 .. mdp-value:: anisotropic
1176 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1177 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1178 respectively. When the off-diagonal compressibilities are set to
1179 zero, a rectangular box will stay rectangular. Beware that
1180 anisotropic scaling can lead to extreme deformation of the
1183 .. mdp-value:: surface-tension
1185 Surface tension coupling for surfaces parallel to the
1186 xy-plane. Uses normal pressure coupling for the `z`-direction,
1187 while the surface tension is coupled to the `x/y` dimensions of
1188 the box. The first :mdp:`ref-p` value is the reference surface
1189 tension times the number of surfaces ``bar nm``, the second
1190 value is the reference `z`-pressure ``bar``. The two
1191 :mdp:`compressibility` values are the compressibility in the
1192 `x/y` and `z` direction respectively. The value for the
1193 `z`-compressibility should be reasonably accurate since it
1194 influences the convergence of the surface-tension, it can also
1195 be set to zero to have a box with constant height.
1200 The frequency for coupling the pressure. The default value of -1
1201 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1202 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1203 Verlet integrators :mdp:`nstpcouple` is set to 1.
1208 The time constant for pressure coupling (one value for all
1211 .. mdp:: compressibility
1214 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1215 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1216 required values is implied by :mdp:`pcoupltype`.
1221 The reference pressure for coupling. The number of required values
1222 is implied by :mdp:`pcoupltype`.
1224 .. mdp:: refcoord-scaling
1228 The reference coordinates for position restraints are not
1229 modified. Note that with this option the virial and pressure
1230 will depend on the absolute positions of the reference
1235 The reference coordinates are scaled with the scaling matrix of
1236 the pressure coupling.
1240 Scale the center of mass of the reference coordinates with the
1241 scaling matrix of the pressure coupling. The vectors of each
1242 reference coordinate to the center of mass are not scaled. Only
1243 one COM is used, even when there are multiple molecules with
1244 position restraints. For calculating the COM of the reference
1245 coordinates in the starting configuration, periodic boundary
1246 conditions are not taken into account.
1252 Simulated annealing is controlled separately for each temperature
1253 group in |Gromacs|. The reference temperature is a piecewise linear
1254 function, but you can use an arbitrary number of points for each
1255 group, and choose either a single sequence or a periodic behaviour for
1256 each group. The actual annealing is performed by dynamically changing
1257 the reference temperature used in the thermostat algorithm selected,
1258 so remember that the system will usually not instantaneously reach the
1259 reference temperature!
1263 Type of annealing for each temperature group
1267 No simulated annealing - just couple to reference temperature value.
1269 .. mdp-value:: single
1271 A single sequence of annealing points. If your simulation is
1272 longer than the time of the last point, the temperature will be
1273 coupled to this constant value after the annealing sequence has
1274 reached the last time point.
1276 .. mdp-value:: periodic
1278 The annealing will start over at the first reference point once
1279 the last reference time is reached. This is repeated until the
1282 .. mdp:: annealing-npoints
1284 A list with the number of annealing reference/control points used
1285 for each temperature group. Use 0 for groups that are not
1286 annealed. The number of entries should equal the number of
1289 .. mdp:: annealing-time
1291 List of times at the annealing reference/control points for each
1292 group. If you are using periodic annealing, the times will be used
1293 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1294 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1295 etc. The number of entries should equal the sum of the numbers
1296 given in :mdp:`annealing-npoints`.
1298 .. mdp:: annealing-temp
1300 List of temperatures at the annealing reference/control points for
1301 each group. The number of entries should equal the sum of the
1302 numbers given in :mdp:`annealing-npoints`.
1304 Confused? OK, let's use an example. Assume you have two temperature
1305 groups, set the group selections to ``annealing = single periodic``,
1306 the number of points of each group to ``annealing-npoints = 3 4``, the
1307 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1308 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1309 will be coupled to 298K at 0ps, but the reference temperature will
1310 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1311 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1312 second group is coupled to 298K at 0ps, it increases linearly to 320K
1313 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1314 decreases to 298K, and then it starts over with the same pattern
1315 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1316 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1326 Do not generate velocities. The velocities are set to zero
1327 when there are no velocities in the input structure file.
1331 Generate velocities in :ref:`gmx grompp` according to a
1332 Maxwell distribution at temperature :mdp:`gen-temp`, with
1333 random seed :mdp:`gen-seed`. This is only meaningful with
1334 :mdp-value:`integrator=md`.
1339 temperature for Maxwell distribution
1344 used to initialize random generator for random velocities,
1345 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1352 .. mdp:: constraints
1354 Controls which bonds in the topology will be converted to rigid
1355 holonomic constraints. Note that typical rigid water models do not
1356 have bonds, but rather a specialized ``[settles]`` directive, so
1357 are not affected by this keyword.
1361 No bonds converted to constraints.
1363 .. mdp-value:: h-bonds
1365 Convert the bonds with H-atoms to constraints.
1367 .. mdp-value:: all-bonds
1369 Convert all bonds to constraints.
1371 .. mdp-value:: h-angles
1373 Convert all bonds to constraints and convert the angles that
1374 involve H-atoms to bond-constraints.
1376 .. mdp-value:: all-angles
1378 Convert all bonds to constraints and all angles to bond-constraints.
1380 .. mdp:: constraint-algorithm
1382 Chooses which solver satisfies any non-SETTLE holonomic
1385 .. mdp-value:: LINCS
1387 LINear Constraint Solver. With domain decomposition the parallel
1388 version P-LINCS is used. The accuracy in set with
1389 :mdp:`lincs-order`, which sets the number of matrices in the
1390 expansion for the matrix inversion. After the matrix inversion
1391 correction the algorithm does an iterative correction to
1392 compensate for lengthening due to rotation. The number of such
1393 iterations can be controlled with :mdp:`lincs-iter`. The root
1394 mean square relative constraint deviation is printed to the log
1395 file every :mdp:`nstlog` steps. If a bond rotates more than
1396 :mdp:`lincs-warnangle` in one step, a warning will be printed
1397 both to the log file and to ``stderr``. LINCS should not be used
1398 with coupled angle constraints.
1400 .. mdp-value:: SHAKE
1402 SHAKE is slightly slower and less stable than LINCS, but does
1403 work with angle constraints. The relative tolerance is set with
1404 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1405 does not support constraints between atoms on different nodes,
1406 thus it can not be used with domain decompositon when inter
1407 charge-group constraints are present. SHAKE can not be used with
1408 energy minimization.
1410 .. mdp:: continuation
1412 This option was formerly known as ``unconstrained-start``.
1416 apply constraints to the start configuration and reset shells
1420 do not apply constraints to the start configuration and do not
1421 reset shells, useful for exact coninuation and reruns
1426 relative tolerance for SHAKE
1428 .. mdp:: lincs-order
1431 Highest order in the expansion of the constraint coupling
1432 matrix. When constraints form triangles, an additional expansion of
1433 the same order is applied on top of the normal expansion only for
1434 the couplings within such triangles. For "normal" MD simulations an
1435 order of 4 usually suffices, 6 is needed for large time-steps with
1436 virtual sites or BD. For accurate energy minimization an order of 8
1437 or more might be required. With domain decomposition, the cell size
1438 is limited by the distance spanned by :mdp:`lincs-order` +1
1439 constraints. When one wants to scale further than this limit, one
1440 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1441 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1442 )* :mdp:`lincs-order` remains constant.
1447 Number of iterations to correct for rotational lengthening in
1448 LINCS. For normal runs a single step is sufficient, but for NVE
1449 runs where you want to conserve energy accurately or for accurate
1450 energy minimization you might want to increase it to 2.
1452 .. mdp:: lincs-warnangle
1455 maximum angle that a bond can rotate before LINCS will complain
1461 bonds are represented by a harmonic potential
1465 bonds are represented by a Morse potential
1468 Energy group exclusions
1469 ^^^^^^^^^^^^^^^^^^^^^^^
1471 .. mdp:: energygrp-excl
1473 Pairs of energy groups for which all non-bonded interactions are
1474 excluded. An example: if you have two energy groups ``Protein`` and
1475 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1476 would give only the non-bonded interactions between the protein and
1477 the solvent. This is especially useful for speeding up energy
1478 calculations with ``mdrun -rerun`` and for excluding interactions
1479 within frozen groups.
1488 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1489 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1490 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1491 used (it is usually best to use semiisotropic pressure coupling
1492 with the ``x/y`` compressibility set to 0, as otherwise the surface
1493 area will change). Walls interact wit the rest of the system
1494 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1495 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1496 monitor the interaction of energy groups with each wall. The center
1497 of mass motion removal will be turned off in the ``z``-direction.
1499 .. mdp:: wall-atomtype
1501 the atom type name in the force field for each wall. By (for
1502 example) defining a special wall atom type in the topology with its
1503 own combination rules, this allows for independent tuning of the
1504 interaction of each atomtype with the walls.
1510 LJ integrated over the volume behind the wall: 9-3 potential
1514 LJ integrated over the wall surface: 10-4 potential
1518 direct LJ potential with the ``z`` distance from the wall
1522 user defined potentials indexed with the ``z`` distance from the
1523 wall, the tables are read analogously to the
1524 :mdp:`energygrp-table` option, where the first name is for a
1525 "normal" energy group and the second name is ``wall0`` or
1526 ``wall1``, only the dispersion and repulsion columns are used
1528 .. mdp:: wall-r-linpot
1531 Below this distance from the wall the potential is continued
1532 linearly and thus the force is constant. Setting this option to a
1533 postive value is especially useful for equilibration when some
1534 atoms are beyond a wall. When the value is <=0 (<0 for
1535 :mdp:`wall-type` =table), a fatal error is generated when atoms
1538 .. mdp:: wall-density
1540 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1541 the number density of the atoms for each wall for wall types 9-3
1544 .. mdp:: wall-ewald-zfac
1547 The scaling factor for the third box vector for Ewald summation
1548 only, the minimum is 2. Ewald summation can only be used with
1549 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1550 ``=3dc``. The empty layer in the box serves to decrease the
1551 unphysical Coulomb interaction between periodic images.
1557 Note that where pulling coordinates are applicable, there can be more
1558 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1559 variables will exist accordingly. Documentation references to things
1560 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1561 applicable pulling coordinate, eg. the second pull coordinate is described by
1562 pull-coord2-vec, pull-coord2-k, and so on.
1568 No center of mass pulling. All the following pull options will
1569 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1574 Center of mass pulling will be applied on 1 or more groups using
1575 1 or more pull coordinates.
1577 .. mdp:: pull-cylinder-r
1580 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1582 .. mdp:: pull-constr-tol
1585 the relative constraint tolerance for constraint pulling
1587 .. mdp:: pull-print-com
1591 do not print the COM for any group
1595 print the COM of all groups for all pull coordinates
1597 .. mdp:: pull-print-ref-value
1601 do not print the reference value for each pull coordinate
1605 print the reference value for each pull coordinate
1607 .. mdp:: pull-print-components
1611 only print the distance for each pull coordinate
1615 print the distance and Cartesian components selected in
1616 :mdp:`pull-coord1-dim`
1618 .. mdp:: pull-nstxout
1621 frequency for writing out the COMs of all the pull group (0 is
1624 .. mdp:: pull-nstfout
1627 frequency for writing out the force of all the pulled group
1630 .. mdp:: pull-pbc-ref-prev-step-com
1634 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1635 treatment of periodic boundary conditions.
1639 Use the COM of the previous step as reference for the treatment
1640 of periodic boundary conditions. The reference is initialized
1641 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1642 be located centrally in the group. Using the COM from the
1643 previous step can be useful if one or more pull groups are large.
1645 .. mdp:: pull-xout-average
1649 Write the instantaneous coordinates for all the pulled groups.
1653 Write the average coordinates (since last output) for all the
1654 pulled groups. N.b., some analysis tools might expect instantaneous
1657 .. mdp:: pull-fout-average
1661 Write the instantaneous force for all the pulled groups.
1665 Write the average force (since last output) for all the
1666 pulled groups. N.b., some analysis tools might expect instantaneous
1669 .. mdp:: pull-ngroups
1672 The number of pull groups, not including the absolute reference
1673 group, when used. Pull groups can be reused in multiple pull
1674 coordinates. Below only the pull options for group 1 are given,
1675 further groups simply increase the group index number.
1677 .. mdp:: pull-ncoords
1680 The number of pull coordinates. Below only the pull options for
1681 coordinate 1 are given, further coordinates simply increase the
1682 coordinate index number.
1684 .. mdp:: pull-group1-name
1686 The name of the pull group, is looked up in the index file or in
1687 the default groups to obtain the atoms involved.
1689 .. mdp:: pull-group1-weights
1691 Optional relative weights which are multiplied with the masses of
1692 the atoms to give the total weight for the COM. The number should
1693 be 0, meaning all 1, or the number of atoms in the pull group.
1695 .. mdp:: pull-group1-pbcatom
1698 The reference atom for the treatment of periodic boundary
1699 conditions inside the group (this has no effect on the treatment of
1700 the pbc between groups). This option is only important when the
1701 diameter of the pull group is larger than half the shortest box
1702 vector. For determining the COM, all atoms in the group are put at
1703 their periodic image which is closest to
1704 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1705 atom (number wise) is used, which is only safe for small groups.
1706 :ref:`gmx grompp` checks that the maximum distance from the reference
1707 atom (specifically chosen, or not) to the other atoms in the group
1708 is not too large. This parameter is not used with
1709 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1710 weighting, which is useful for a group of molecules in a periodic
1711 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1714 .. mdp:: pull-coord1-type
1716 .. mdp-value:: umbrella
1718 Center of mass pulling using an umbrella potential between the
1719 reference group and one or more groups.
1721 .. mdp-value:: constraint
1723 Center of mass pulling using a constraint between the reference
1724 group and one or more groups. The setup is identical to the
1725 option umbrella, except for the fact that a rigid constraint is
1726 applied instead of a harmonic potential.
1728 .. mdp-value:: constant-force
1730 Center of mass pulling using a linear potential and therefore a
1731 constant force. For this option there is no reference position
1732 and therefore the parameters :mdp:`pull-coord1-init` and
1733 :mdp:`pull-coord1-rate` are not used.
1735 .. mdp-value:: flat-bottom
1737 At distances above :mdp:`pull-coord1-init` a harmonic potential
1738 is applied, otherwise no potential is applied.
1740 .. mdp-value:: flat-bottom-high
1742 At distances below :mdp:`pull-coord1-init` a harmonic potential
1743 is applied, otherwise no potential is applied.
1745 .. mdp-value:: external-potential
1747 An external potential that needs to be provided by another
1750 .. mdp:: pull-coord1-potential-provider
1752 The name of the external module that provides the potential for
1753 the case where :mdp:`pull-coord1-type` is external-potential.
1755 .. mdp:: pull-coord1-geometry
1757 .. mdp-value:: distance
1759 Pull along the vector connecting the two groups. Components can
1760 be selected with :mdp:`pull-coord1-dim`.
1762 .. mdp-value:: direction
1764 Pull in the direction of :mdp:`pull-coord1-vec`.
1766 .. mdp-value:: direction-periodic
1768 As :mdp-value:`pull-coord1-geometry=direction`, but allows the distance to be larger
1769 than half the box size. With this geometry the box should not be
1770 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1771 the pull force is not added to virial.
1773 .. mdp-value:: direction-relative
1775 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1776 that points from the COM of a third to the COM of a fourth pull
1777 group. This means that 4 groups need to be supplied in
1778 :mdp:`pull-coord1-groups`. Note that the pull force will give
1779 rise to a torque on the pull vector, which is turn leads to
1780 forces perpendicular to the pull vector on the two groups
1781 defining the vector. If you want a pull group to move between
1782 the two groups defining the vector, simply use the union of
1783 these two groups as the reference group.
1785 .. mdp-value:: cylinder
1787 Designed for pulling with respect to a layer where the reference
1788 COM is given by a local cylindrical part of the reference group.
1789 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1790 the first of the two groups in :mdp:`pull-coord1-groups` a
1791 cylinder is selected around the axis going through the COM of
1792 the second group with direction :mdp:`pull-coord1-vec` with
1793 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1794 continously to zero as the radial distance goes from 0 to
1795 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1796 dependence gives rise to radial forces on both pull groups.
1797 Note that the radius should be smaller than half the box size.
1798 For tilted cylinders they should be even smaller than half the
1799 box size since the distance of an atom in the reference group
1800 from the COM of the pull group has both a radial and an axial
1801 component. This geometry is not supported with constraint
1804 .. mdp-value:: angle
1806 Pull along an angle defined by four groups. The angle is
1807 defined as the angle between two vectors: the vector connecting
1808 the COM of the first group to the COM of the second group and
1809 the vector connecting the COM of the third group to the COM of
1812 .. mdp-value:: angle-axis
1814 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1815 Thus, only the two groups that define the first vector need to be given.
1817 .. mdp-value:: dihedral
1819 Pull along a dihedral angle defined by six groups. These pairwise
1820 define three vectors: the vector connecting the COM of group 1
1821 to the COM of group 2, the COM of group 3 to the COM of group 4,
1822 and the COM of group 5 to the COM group 6. The dihedral angle is
1823 then defined as the angle between two planes: the plane spanned by the
1824 the two first vectors and the plane spanned the two last vectors.
1827 .. mdp:: pull-coord1-groups
1829 The group indices on which this pull coordinate will operate.
1830 The number of group indices required is geometry dependent.
1831 The first index can be 0, in which case an
1832 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1833 absolute reference the system is no longer translation invariant
1834 and one should think about what to do with the center of mass
1837 .. mdp:: pull-coord1-dim
1840 Selects the dimensions that this pull coordinate acts on and that
1841 are printed to the output files when
1842 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1843 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1844 components set to Y contribute to the distance. Thus setting this
1845 to Y Y N results in a distance in the x/y plane. With other
1846 geometries all dimensions with non-zero entries in
1847 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1848 dimensions only affect the output.
1850 .. mdp:: pull-coord1-origin
1853 The pull reference position for use with an absolute reference.
1855 .. mdp:: pull-coord1-vec
1858 The pull direction. :ref:`gmx grompp` normalizes the vector.
1860 .. mdp:: pull-coord1-start
1864 do not modify :mdp:`pull-coord1-init`
1868 add the COM distance of the starting conformation to
1869 :mdp:`pull-coord1-init`
1871 .. mdp:: pull-coord1-init
1874 The reference distance or reference angle at t=0.
1876 .. mdp:: pull-coord1-rate
1878 (0) [nm/ps] or [deg/ps]
1879 The rate of change of the reference position or reference angle.
1881 .. mdp:: pull-coord1-k
1883 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1884 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1885 The force constant. For umbrella pulling this is the harmonic force
1886 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1887 for angles). For constant force pulling this is the
1888 force constant of the linear potential, and thus the negative (!)
1889 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1890 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1891 Note that for angles the force constant is expressed in terms of radians
1892 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1894 .. mdp:: pull-coord1-kB
1896 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1897 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1898 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1899 :mdp:`free-energy` is turned on. The force constant is then (1 -
1900 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1902 AWH adaptive biasing
1903 ^^^^^^^^^^^^^^^^^^^^
1913 Adaptively bias a reaction coordinate using the AWH method and estimate
1914 the corresponding PMF. The PMF and other AWH data are written to energy
1915 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1916 the ``gmx awh`` tool. The AWH coordinate can be
1917 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1918 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1919 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1922 .. mdp:: awh-potential
1924 .. mdp-value:: convolved
1926 The applied biasing potential is the convolution of the bias function and a
1927 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1928 in a smooth potential function and force. The resolution of the potential is set
1929 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1931 .. mdp-value:: umbrella
1933 The potential bias is applied by controlling the position of an harmonic potential
1934 using Monte-Carlo sampling. The force constant is set with
1935 :mdp:`awh1-dim1-force-constant`. The umbrella location
1936 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1937 There are no advantages to using an umbrella.
1938 This option is mainly for comparison and testing purposes.
1940 .. mdp:: awh-share-multisim
1944 AWH will not share biases across simulations started with
1945 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1949 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1950 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1951 with the biases with the same :mdp:`awh1-share-group` value.
1952 The simulations should have the same AWH settings for sharing to make sense.
1953 :ref:`gmx mdrun` will check whether the simulations are technically
1954 compatible for sharing, but the user should check that bias sharing
1955 physically makes sense.
1959 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1960 where -1 indicates to generate a seed. Only used with
1961 :mdp-value:`awh-potential=umbrella`.
1966 Number of steps between printing AWH data to the energy file, should be
1967 a multiple of :mdp:`nstenergy`.
1969 .. mdp:: awh-nstsample
1972 Number of steps between sampling of the coordinate value. This sampling
1973 is the basis for updating the bias and estimating the PMF and other AWH observables.
1975 .. mdp:: awh-nsamples-update
1978 The number of coordinate samples used for each AWH update.
1979 The update interval in steps is :mdp:`awh-nstsample` times this value.
1984 The number of biases, each acting on its own coordinate.
1985 The following options should be specified
1986 for each bias although below only the options for bias number 1 is shown. Options for
1987 other bias indices are obtained by replacing '1' by the bias index.
1989 .. mdp:: awh1-error-init
1991 (10.0) [kJ mol\ :sup:`-1`]
1992 Estimated initial average error of the PMF for this bias. This value together with the
1993 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1994 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1996 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1997 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1998 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1999 then :mdp:`awh1-error-init` should reflect that knowledge.
2001 .. mdp:: awh1-growth
2003 .. mdp-value:: exp-linear
2005 Each bias keeps a reference weight histogram for the coordinate samples.
2006 Its size sets the magnitude of the bias function and free energy estimate updates
2007 (few samples corresponds to large updates and vice versa).
2008 Thus, its growth rate sets the maximum convergence rate.
2009 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
2010 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
2011 The initial stage is typically necessary for efficient convergence when starting a new simulation where
2012 high free energy barriers have not yet been flattened by the bias.
2014 .. mdp-value:: linear
2016 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
2017 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
2018 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
2020 .. mdp:: awh1-equilibrate-histogram
2024 Do not equilibrate histogram.
2028 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
2029 histogram of sampled weights is following the target distribution closely enough (specifically,
2030 at least 80% of the target region needs to have a local relative error of less than 20%). This
2031 option would typically only be used when :mdp:`awh1-share-group` > 0
2032 and the initial configurations poorly represent the target
2035 .. mdp:: awh1-target
2037 .. mdp-value:: constant
2039 The bias is tuned towards a constant (uniform) coordinate distribution
2040 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
2042 .. mdp-value:: cutoff
2044 Similar to :mdp-value:`awh1-target=constant`, but the target
2045 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
2046 where F is the free energy relative to the estimated global minimum.
2047 This provides a smooth switch of a flat target distribution in
2048 regions with free energy lower than the cut-off to a Boltzmann
2049 distribution in regions with free energy higher than the cut-off.
2051 .. mdp-value:: boltzmann
2053 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
2054 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
2055 would give the same coordinate distribution as sampling with a simulation temperature
2058 .. mdp-value:: local-boltzmann
2060 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
2061 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
2062 change of the bias only depends on the local sampling. This local convergence property is
2063 only compatible with :mdp-value:`awh1-growth=linear`, since for
2064 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
2066 .. mdp:: awh1-target-beta-scaling
2069 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
2070 it is the unitless beta scaling factor taking values in (0,1).
2072 .. mdp:: awh1-target-cutoff
2074 (0) [kJ mol\ :sup:`-1`]
2075 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2077 .. mdp:: awh1-user-data
2081 Initialize the PMF and target distribution with default values.
2085 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2086 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2087 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2088 The file name can be changed with the ``-awh`` option.
2089 The first :mdp:`awh1-ndim` columns of
2090 each input file should contain the coordinate values, such that each row defines a point in
2091 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
2092 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2093 be in the same column as written by :ref:`gmx awh`.
2095 .. mdp:: awh1-share-group
2099 Do not share the bias.
2101 .. mdp-value:: positive
2103 Share the bias and PMF estimates within and/or between simulations.
2104 Within a simulation, the bias will be shared between biases that have the
2105 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2106 With :mdp-value:`awh-share-multisim=yes` and
2107 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2108 Sharing may increase convergence initially, although the starting configurations
2109 can be critical, especially when sharing between many biases.
2110 Currently, positive group values should start at 1 and increase
2111 by 1 for each subsequent bias that is shared.
2116 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2117 The following options should be specified for each such dimension. Below only
2118 the options for dimension number 1 is shown. Options for other dimension indices are
2119 obtained by replacing '1' by the dimension index.
2121 .. mdp:: awh1-dim1-coord-provider
2125 The module providing the reaction coordinate for this dimension.
2126 Currently AWH can only act on pull coordinates.
2128 .. mdp:: awh1-dim1-coord-index
2131 Index of the pull coordinate defining this coordinate dimension.
2133 .. mdp:: awh1-dim1-force-constant
2135 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2136 Force constant for the (convolved) umbrella potential(s) along this
2137 coordinate dimension.
2139 .. mdp:: awh1-dim1-start
2142 Start value of the sampling interval along this dimension. The range of allowed
2143 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2144 For periodic geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2145 is allowed. The interval will then wrap around from +period/2 to -period/2.
2147 .. mdp:: awh1-dim1-end
2150 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2152 .. mdp:: awh1-dim1-period
2155 The period of this reaction coordinate, use 0 when the coordinate is not periodic.
2157 .. mdp:: awh1-dim1-diffusion
2159 (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps]
2160 Estimated diffusion constant for this coordinate dimension determining the initial
2161 biasing rate. This needs only be a rough estimate and should not critically
2162 affect the results unless it is set to something very low, leading to slow convergence,
2163 or very high, forcing the system far from equilibrium. Not setting this value
2164 explicitly generates a warning.
2166 .. mdp:: awh1-dim1-cover-diameter
2169 Diameter that needs to be sampled by a single simulation around a coordinate value
2170 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2171 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2172 across each coordinate value.
2173 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2174 (:mdp:`awh1-share-group`>0).
2175 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2176 for many sharing simulations does not guarantee transitions across free energy barriers.
2177 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2178 has independently sampled the whole interval.
2183 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2184 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2185 that can be used to achieve such a rotation.
2191 No enforced rotation will be applied. All enforced rotation options will
2192 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2197 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2198 under the :mdp:`rot-group0` option.
2200 .. mdp:: rot-ngroups
2203 Number of rotation groups.
2207 Name of rotation group 0 in the index file.
2212 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2213 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2214 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2219 Use mass weighted rotation group positions.
2224 Rotation vector, will get normalized.
2229 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2233 (0) [degree ps\ :sup:`-1`]
2234 Reference rotation rate of group 0.
2238 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2239 Force constant for group 0.
2241 .. mdp:: rot-slab-dist0
2244 Slab distance, if a flexible axis rotation type was chosen.
2246 .. mdp:: rot-min-gauss0
2249 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2250 (for the flexible axis potentials).
2254 (0.0001) [nm\ :sup:`2`]
2255 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2257 .. mdp:: rot-fit-method0
2260 Fitting method when determining the actual angle of a rotation group
2261 (can be one of ``rmsd``, ``norm``, or ``potential``).
2263 .. mdp:: rot-potfit-nsteps0
2266 For fit type ``potential``, the number of angular positions around the reference angle for which the
2267 rotation potential is evaluated.
2269 .. mdp:: rot-potfit-step0
2272 For fit type ``potential``, the distance in degrees between two angular positions.
2274 .. mdp:: rot-nstrout
2277 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2278 and the rotation potential energy.
2280 .. mdp:: rot-nstsout
2283 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2293 ignore distance restraint information in topology file
2295 .. mdp-value:: simple
2297 simple (per-molecule) distance restraints.
2299 .. mdp-value:: ensemble
2301 distance restraints over an ensemble of molecules in one
2302 simulation box. Normally, one would perform ensemble averaging
2303 over multiple simulations, using ``mdrun
2304 -multidir``. The environment
2305 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2306 within each ensemble (usually equal to the number of directories
2307 supplied to ``mdrun -multidir``).
2309 .. mdp:: disre-weighting
2311 .. mdp-value:: equal
2313 divide the restraint force equally over all atom pairs in the
2316 .. mdp-value:: conservative
2318 the forces are the derivative of the restraint potential, this
2319 results in an weighting of the atom pairs to the reciprocal
2320 seventh power of the displacement. The forces are conservative
2321 when :mdp:`disre-tau` is zero.
2323 .. mdp:: disre-mixed
2327 the violation used in the calculation of the restraint force is
2328 the time-averaged violation
2332 the violation used in the calculation of the restraint force is
2333 the square root of the product of the time-averaged violation
2334 and the instantaneous violation
2338 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2339 force constant for distance restraints, which is multiplied by a
2340 (possibly) different factor for each restraint given in the `fac`
2341 column of the interaction in the topology file.
2346 time constant for distance restraints running average. A value of
2347 zero turns off time averaging.
2349 .. mdp:: nstdisreout
2352 period between steps when the running time-averaged and
2353 instantaneous distances of all atom pairs involved in restraints
2354 are written to the energy file (can make the energy file very
2361 ignore orientation restraint information in topology file
2365 use orientation restraints, ensemble averaging can be performed
2366 with ``mdrun -multidir``
2370 (0) [kJ mol\ :sup:`-1`]
2371 force constant for orientation restraints, which is multiplied by a
2372 (possibly) different weight factor for each restraint, can be set
2373 to zero to obtain the orientations from a free simulation
2378 time constant for orientation restraints running average. A value
2379 of zero turns off time averaging.
2381 .. mdp:: orire-fitgrp
2383 fit group for orientation restraining. This group of atoms is used
2384 to determine the rotation **R** of the system with respect to the
2385 reference orientation. The reference orientation is the starting
2386 conformation of the first subsystem. For a protein, backbone is a
2389 .. mdp:: nstorireout
2392 period between steps when the running time-averaged and
2393 instantaneous orientations for all restraints, and the molecular
2394 order tensor are written to the energy file (can make the energy
2398 Free energy calculations
2399 ^^^^^^^^^^^^^^^^^^^^^^^^
2401 .. mdp:: free-energy
2405 Only use topology A.
2409 Interpolate between topology A (lambda=0) to topology B
2410 (lambda=1) and write the derivative of the Hamiltonian with
2411 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2412 or the Hamiltonian differences with respect to other lambda
2413 values (as specified with foreign lambda) to the energy file
2414 and/or to ``dhdl.xvg``, where they can be processed by, for
2415 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2416 are interpolated linearly as described in the manual. When
2417 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2418 used for the LJ and Coulomb interactions.
2422 Turns on expanded ensemble simulation, where the alchemical state
2423 becomes a dynamic variable, allowing jumping between different
2424 Hamiltonians. See the expanded ensemble options for controlling how
2425 expanded ensemble simulations are performed. The different
2426 Hamiltonians used in expanded ensemble simulations are defined by
2427 the other free energy options.
2429 .. mdp:: init-lambda
2432 starting value for lambda (float). Generally, this should only be
2433 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2434 other cases, :mdp:`init-lambda-state` should be specified
2435 instead. Must be greater than or equal to 0.
2437 .. mdp:: delta-lambda
2440 increment per time step for lambda
2442 .. mdp:: init-lambda-state
2445 starting value for the lambda state (integer). Specifies which
2446 columm of the lambda vector (:mdp:`coul-lambdas`,
2447 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2448 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2449 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2450 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2451 the first column, and so on.
2453 .. mdp:: fep-lambdas
2456 Zero, one or more lambda values for which Delta H values will be
2457 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2458 steps. Values must be between 0 and 1. Free energy differences
2459 between different lambda values can then be determined with
2460 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2461 other -lambdas keywords because all components of the lambda vector
2462 that are not specified will use :mdp:`fep-lambdas` (including
2463 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2465 .. mdp:: coul-lambdas
2468 Zero, one or more lambda values for which Delta H values will be
2469 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2470 steps. Values must be between 0 and 1. Only the electrostatic
2471 interactions are controlled with this component of the lambda
2472 vector (and only if the lambda=0 and lambda=1 states have differing
2473 electrostatic interactions).
2475 .. mdp:: vdw-lambdas
2478 Zero, one or more lambda values for which Delta H values will be
2479 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2480 steps. Values must be between 0 and 1. Only the van der Waals
2481 interactions are controlled with this component of the lambda
2484 .. mdp:: bonded-lambdas
2487 Zero, one or more lambda values for which Delta H values will be
2488 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2489 steps. Values must be between 0 and 1. Only the bonded interactions
2490 are controlled with this component of the lambda vector.
2492 .. mdp:: restraint-lambdas
2495 Zero, one or more lambda values for which Delta H values will be
2496 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2497 steps. Values must be between 0 and 1. Only the restraint
2498 interactions: dihedral restraints, and the pull code restraints are
2499 controlled with this component of the lambda vector.
2501 .. mdp:: mass-lambdas
2504 Zero, one or more lambda values for which Delta H values will be
2505 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2506 steps. Values must be between 0 and 1. Only the particle masses are
2507 controlled with this component of the lambda vector.
2509 .. mdp:: temperature-lambdas
2512 Zero, one or more lambda values for which Delta H values will be
2513 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2514 steps. Values must be between 0 and 1. Only the temperatures
2515 controlled with this component of the lambda vector. Note that
2516 these lambdas should not be used for replica exchange, only for
2517 simulated tempering.
2519 .. mdp:: calc-lambda-neighbors
2522 Controls the number of lambda values for which Delta H values will
2523 be calculated and written out, if :mdp:`init-lambda-state` has
2524 been set. A positive value will limit the number of lambda points
2525 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2526 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2527 has a value of 2, energies for lambda points 3-7 will be calculated
2528 and writen out. A value of -1 means all lambda points will be
2529 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2530 1 is sufficient, while for MBAR -1 should be used.
2535 the soft-core alpha parameter, a value of 0 results in linear
2536 interpolation of the LJ and Coulomb interactions
2541 the power of the radial term in the soft-core equation. Possible
2542 values are 6 and 48. 6 is more standard, and is the default. When
2543 48 is used, then sc-alpha should generally be much lower (between
2549 Whether to apply the soft-core free energy interaction
2550 transformation to the Columbic interaction of a molecule. Default
2551 is no, as it is generally more efficient to turn off the Coulomic
2552 interactions linearly before turning off the van der Waals
2553 interactions. Note that it is only taken into account when lambda
2554 states are used, not with :mdp:`couple-lambda0` /
2555 :mdp:`couple-lambda1`, and you can still turn off soft-core
2556 interactions by setting :mdp:`sc-alpha` to 0.
2561 the power for lambda in the soft-core function, only the values 1
2567 the soft-core sigma for particles which have a C6 or C12 parameter
2568 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2570 .. mdp:: couple-moltype
2572 Here one can supply a molecule type (as defined in the topology)
2573 for calculating solvation or coupling free energies. There is a
2574 special option ``system`` that couples all molecule types in the
2575 system. This can be useful for equilibrating a system starting from
2576 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2577 on. The Van der Waals interactions and/or charges in this molecule
2578 type can be turned on or off between lambda=0 and lambda=1,
2579 depending on the settings of :mdp:`couple-lambda0` and
2580 :mdp:`couple-lambda1`. If you want to decouple one of several
2581 copies of a molecule, you need to copy and rename the molecule
2582 definition in the topology.
2584 .. mdp:: couple-lambda0
2586 .. mdp-value:: vdw-q
2588 all interactions are on at lambda=0
2592 the charges are zero (no Coulomb interactions) at lambda=0
2596 the Van der Waals interactions are turned at lambda=0; soft-core
2597 interactions will be required to avoid singularities
2601 the Van der Waals interactions are turned off and the charges
2602 are zero at lambda=0; soft-core interactions will be required to
2603 avoid singularities.
2605 .. mdp:: couple-lambda1
2607 analogous to :mdp:`couple-lambda1`, but for lambda=1
2609 .. mdp:: couple-intramol
2613 All intra-molecular non-bonded interactions for moleculetype
2614 :mdp:`couple-moltype` are replaced by exclusions and explicit
2615 pair interactions. In this manner the decoupled state of the
2616 molecule corresponds to the proper vacuum state without
2617 periodicity effects.
2621 The intra-molecular Van der Waals and Coulomb interactions are
2622 also turned on/off. This can be useful for partitioning
2623 free-energies of relatively large molecules, where the
2624 intra-molecular non-bonded interactions might lead to
2625 kinetically trapped vacuum conformations. The 1-4 pair
2626 interactions are not turned off.
2631 the frequency for writing dH/dlambda and possibly Delta H to
2632 dhdl.xvg, 0 means no ouput, should be a multiple of
2633 :mdp:`nstcalcenergy`.
2635 .. mdp:: dhdl-derivatives
2639 If yes (the default), the derivatives of the Hamiltonian with
2640 respect to lambda at each :mdp:`nstdhdl` step are written
2641 out. These values are needed for interpolation of linear energy
2642 differences with :ref:`gmx bar` (although the same can also be
2643 achieved with the right foreign lambda setting, that may not be as
2644 flexible), or with thermodynamic integration
2646 .. mdp:: dhdl-print-energy
2650 Include either the total or the potential energy in the dhdl
2651 file. Options are 'no', 'potential', or 'total'. This information
2652 is needed for later free energy analysis if the states of interest
2653 are at different temperatures. If all states are at the same
2654 temperature, this information is not needed. 'potential' is useful
2655 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2656 file. When rerunning from an existing trajectory, the kinetic
2657 energy will often not be correct, and thus one must compute the
2658 residual free energy from the potential alone, with the kinetic
2659 energy component computed analytically.
2661 .. mdp:: separate-dhdl-file
2665 The free energy values that are calculated (as specified with
2666 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2667 written out to a separate file, with the default name
2668 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2673 The free energy values are written out to the energy output file
2674 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2675 steps), where they can be extracted with :ref:`gmx energy` or
2676 used directly with :ref:`gmx bar`.
2678 .. mdp:: dh-hist-size
2681 If nonzero, specifies the size of the histogram into which the
2682 Delta H values (specified with foreign lambda) and the derivative
2683 dH/dl values are binned, and written to ener.edr. This can be used
2684 to save disk space while calculating free energy differences. One
2685 histogram gets written for each foreign lambda and two for the
2686 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2687 histogram settings (too small size or too wide bins) can introduce
2688 errors. Do not use histograms unless you're certain you need it.
2690 .. mdp:: dh-hist-spacing
2693 Specifies the bin width of the histograms, in energy units. Used in
2694 conjunction with :mdp:`dh-hist-size`. This size limits the
2695 accuracy with which free energies can be calculated. Do not use
2696 histograms unless you're certain you need it.
2699 Expanded Ensemble calculations
2700 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2702 .. mdp:: nstexpanded
2704 The number of integration steps beween attempted moves changing the
2705 system Hamiltonian in expanded ensemble simulations. Must be a
2706 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2713 No Monte Carlo in state space is performed.
2715 .. mdp-value:: metropolis-transition
2717 Uses the Metropolis weights to update the expanded ensemble
2718 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2721 .. mdp-value:: barker-transition
2723 Uses the Barker transition critera to update the expanded
2724 ensemble weight of each state i, defined by exp(-beta_new
2725 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2727 .. mdp-value:: wang-landau
2729 Uses the Wang-Landau algorithm (in state space, not energy
2730 space) to update the expanded ensemble weights.
2732 .. mdp-value:: min-variance
2734 Uses the minimum variance updating method of Escobedo et al. to
2735 update the expanded ensemble weights. Weights will not be the
2736 free energies, but will rather emphasize states that need more
2737 sampling to give even uncertainty.
2739 .. mdp:: lmc-mc-move
2743 No Monte Carlo in state space is performed.
2745 .. mdp-value:: metropolis-transition
2747 Randomly chooses a new state up or down, then uses the
2748 Metropolis critera to decide whether to accept or reject:
2749 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2751 .. mdp-value:: barker-transition
2753 Randomly chooses a new state up or down, then uses the Barker
2754 transition critera to decide whether to accept or reject:
2755 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2757 .. mdp-value:: gibbs
2759 Uses the conditional weights of the state given the coordinate
2760 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2763 .. mdp-value:: metropolized-gibbs
2765 Uses the conditional weights of the state given the coordinate
2766 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2767 to move to, EXCLUDING the current state, then uses a rejection
2768 step to ensure detailed balance. Always more efficient that
2769 Gibbs, though only marginally so in many situations, such as
2770 when only the nearest neighbors have decent phase space
2776 random seed to use for Monte Carlo moves in state space. When
2777 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2779 .. mdp:: mc-temperature
2781 Temperature used for acceptance/rejection for Monte Carlo moves. If
2782 not specified, the temperature of the simulation specified in the
2783 first group of :mdp:`ref-t` is used.
2788 The cutoff for the histogram of state occupancies to be reset, and
2789 the free energy incrementor to be changed from delta to delta *
2790 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2791 each histogram) / (average number of samples at each
2792 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2793 histogram is only considered flat if all Nratio > 0.8 AND
2794 simultaneously all 1/Nratio > 0.8.
2799 Each time the histogram is considered flat, then the current value
2800 of the Wang-Landau incrementor for the free energies is multiplied
2801 by :mdp:`wl-scale`. Value must be between 0 and 1.
2803 .. mdp:: init-wl-delta
2806 The initial value of the Wang-Landau incrementor in kT. Some value
2807 near 1 kT is usually most efficient, though sometimes a value of
2808 2-3 in units of kT works better if the free energy differences are
2811 .. mdp:: wl-oneovert
2814 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2815 the large sample limit. There is significant evidence that the
2816 standard Wang-Landau algorithms in state space presented here
2817 result in free energies getting 'burned in' to incorrect values
2818 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2819 then when the incrementor becomes less than 1/N, where N is the
2820 mumber of samples collected (and thus proportional to the data
2821 collection time, hence '1 over t'), then the Wang-Lambda
2822 incrementor is set to 1/N, decreasing every step. Once this occurs,
2823 :mdp:`wl-ratio` is ignored, but the weights will still stop
2824 updating when the equilibration criteria set in
2825 :mdp:`lmc-weights-equil` is achieved.
2827 .. mdp:: lmc-repeats
2830 Controls the number of times that each Monte Carlo swap type is
2831 performed each iteration. In the limit of large numbers of Monte
2832 Carlo repeats, then all methods converge to Gibbs sampling. The
2833 value will generally not need to be different from 1.
2835 .. mdp:: lmc-gibbsdelta
2838 Limit Gibbs sampling to selected numbers of neighboring states. For
2839 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2840 sampling over all of the states that are defined. A positive value
2841 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2842 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2843 value of -1 means that all states are considered. For less than 100
2844 states, it is probably not that expensive to include all states.
2846 .. mdp:: lmc-forced-nstart
2849 Force initial state space sampling to generate weights. In order to
2850 come up with reasonable initial weights, this setting allows the
2851 simulation to drive from the initial to the final lambda state,
2852 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2853 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2854 sufficiently long (thousands of steps, perhaps), then the weights
2855 will be close to correct. However, in most cases, it is probably
2856 better to simply run the standard weight equilibration algorithms.
2858 .. mdp:: nst-transition-matrix
2861 Frequency of outputting the expanded ensemble transition matrix. A
2862 negative number means it will only be printed at the end of the
2865 .. mdp:: symmetrized-transition-matrix
2868 Whether to symmetrize the empirical transition matrix. In the
2869 infinite limit the matrix will be symmetric, but will diverge with
2870 statistical noise for short timescales. Forced symmetrization, by
2871 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2872 like the existence of (small magnitude) negative eigenvalues.
2874 .. mdp:: mininum-var-min
2877 The min-variance strategy (option of :mdp:`lmc-stats` is only
2878 valid for larger number of samples, and can get stuck if too few
2879 samples are used at each state. :mdp:`mininum-var-min` is the
2880 minimum number of samples that each state that are allowed before
2881 the min-variance strategy is activated if selected.
2883 .. mdp:: init-lambda-weights
2885 The initial weights (free energies) used for the expanded ensemble
2886 states. Default is a vector of zero weights. format is similar to
2887 the lambda vector settings in :mdp:`fep-lambdas`, except the
2888 weights can be any floating point number. Units are kT. Its length
2889 must match the lambda vector lengths.
2891 .. mdp:: lmc-weights-equil
2895 Expanded ensemble weights continue to be updated throughout the
2900 The input expanded ensemble weights are treated as equilibrated,
2901 and are not updated throughout the simulation.
2903 .. mdp-value:: wl-delta
2905 Expanded ensemble weight updating is stopped when the
2906 Wang-Landau incrementor falls below this value.
2908 .. mdp-value:: number-all-lambda
2910 Expanded ensemble weight updating is stopped when the number of
2911 samples at all of the lambda states is greater than this value.
2913 .. mdp-value:: number-steps
2915 Expanded ensemble weight updating is stopped when the number of
2916 steps is greater than the level specified by this value.
2918 .. mdp-value:: number-samples
2920 Expanded ensemble weight updating is stopped when the number of
2921 total samples across all lambda states is greater than the level
2922 specified by this value.
2924 .. mdp-value:: count-ratio
2926 Expanded ensemble weight updating is stopped when the ratio of
2927 samples at the least sampled lambda state and most sampled
2928 lambda state greater than this value.
2930 .. mdp:: simulated-tempering
2933 Turn simulated tempering on or off. Simulated tempering is
2934 implemented as expanded ensemble sampling with different
2935 temperatures instead of different Hamiltonians.
2937 .. mdp:: sim-temp-low
2940 Low temperature for simulated tempering.
2942 .. mdp:: sim-temp-high
2945 High temperature for simulated tempering.
2947 .. mdp:: simulated-tempering-scaling
2949 Controls the way that the temperatures at intermediate lambdas are
2950 calculated from the :mdp:`temperature-lambdas` part of the lambda
2953 .. mdp-value:: linear
2955 Linearly interpolates the temperatures using the values of
2956 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2957 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2958 a temperature of 350. A nonlinear set of temperatures can always
2959 be implemented with uneven spacing in lambda.
2961 .. mdp-value:: geometric
2963 Interpolates temperatures geometrically between
2964 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2965 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2966 :mdp:`sim-temp-low`) raised to the power of
2967 (i/(ntemps-1)). This should give roughly equal exchange for
2968 constant heat capacity, though of course things simulations that
2969 involve protein folding have very high heat capacity peaks.
2971 .. mdp-value:: exponential
2973 Interpolates temperatures exponentially between
2974 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2975 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2976 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2977 (i))-1)/(exp(1.0)-i)).
2985 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2986 in groups Protein and Sol will experience constant acceleration as
2987 specified in the :mdp:`accelerate` line
2991 (0) [nm ps\ :sup:`-2`]
2992 acceleration for :mdp:`acc-grps`; x, y and z for each group
2993 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2994 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
2999 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
3000 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
3001 specifies for which dimension(s) the freezing applies. To avoid
3002 spurious contributions to the virial and pressure due to large
3003 forces between completely frozen atoms you need to use energy group
3004 exclusions, this also saves computing time. Note that coordinates
3005 of frozen atoms are not scaled by pressure-coupling algorithms.
3009 dimensions for which groups in :mdp:`freezegrps` should be frozen,
3010 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
3011 N N N N`` means that particles in the first group can move only in
3012 Z direction. The particles in the second group can move in any
3015 .. mdp:: cos-acceleration
3017 (0) [nm ps\ :sup:`-2`]
3018 the amplitude of the acceleration profile for calculating the
3019 viscosity. The acceleration is in the X-direction and the magnitude
3020 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
3021 added to the energy file: the amplitude of the velocity profile and
3026 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
3027 The velocities of deformation for the box elements: a(x) b(y) c(z)
3028 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
3029 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
3030 elements are corrected for periodicity. The coordinates are
3031 transformed accordingly. Frozen degrees of freedom are (purposely)
3032 also transformed. The time ts is set to t at the first step and at
3033 steps at which x and v are written to trajectory to ensure exact
3034 restarts. Deformation can be used together with semiisotropic or
3035 anisotropic pressure coupling when the appropriate
3036 compressibilities are set to zero. The diagonal elements can be
3037 used to strain a solid. The off-diagonal elements can be used to
3038 shear a solid or a liquid.
3044 .. mdp:: electric-field-x ; electric-field-y ; electric-field-z
3046 Here you can specify an electric field that optionally can be
3047 alternating and pulsed. The general expression for the field
3048 has the form of a gaussian laser pulse:
3050 E(t) = E0 exp ( -(t-t0)\ :sup:`2`/(2 sigma\ :sup:`2`) ) cos(omega (t-t0))
3052 For example, the four parameters for direction x are set in the
3053 three fields of ``electric-field-x`` (and similar for y and z)
3056 electric-field-x = E0 omega t0 sigma
3058 In the special case that sigma = 0, the exponential term is omitted
3059 and only the cosine term is used. If also omega = 0 a static
3060 electric field is applied.
3062 More details in Carl Caleman and David van der Spoel: Picosecond
3063 Melting of Ice by an Infrared Laser Pulse - A Simulation Study.
3064 Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008)
3068 Mixed quantum/classical molecular dynamics
3069 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3079 Do a QM/MM simulation. Several groups can be described at
3080 different QM levels separately. These are specified in the
3081 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
3082 initio* theory at which the groups are described is specified by
3083 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
3084 groups at different levels of theory is only possible with the
3085 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
3089 groups to be descibed at the QM level (works also in case of MiMiC QM/MM)
3093 .. mdp-value:: normal
3095 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
3096 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
3097 *ab initio* theory. The rest of the system is described at the
3098 MM level. The QM and MM subsystems interact as follows: MM point
3099 charges are included in the QM one-electron hamiltonian and all
3100 Lennard-Jones interactions are described at the MM level.
3102 .. mdp-value:: ONIOM
3104 The interaction between the subsystem is described using the
3105 ONIOM method by Morokuma and co-workers. There can be more than
3106 one :mdp:`QMMM-grps` each modeled at a different level of QM
3107 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
3112 Method used to compute the energy and gradients on the QM
3113 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
3114 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
3115 included in the active space is specified by :mdp:`CASelectrons`
3116 and :mdp:`CASorbitals`.
3121 Basis set used to expand the electronic wavefuntion. Only Gaussian
3122 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3123 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
3128 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
3129 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
3130 layer needs to be specified separately.
3135 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
3136 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
3137 needs to be specified separately.
3139 .. mdp:: CASorbitals
3142 The number of orbitals to be included in the active space when
3143 doing a CASSCF computation.
3145 .. mdp:: CASelectrons
3148 The number of electrons to be included in the active space when
3149 doing a CASSCF computation.
3155 No surface hopping. The system is always in the electronic
3160 Do a QM/MM MD simulation on the excited state-potential energy
3161 surface and enforce a *diabatic* hop to the ground-state when
3162 the system hits the conical intersection hyperline in the course
3163 the simulation. This option only works in combination with the
3167 Computational Electrophysiology
3168 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3169 Use these options to switch on and control ion/water position exchanges in "Computational
3170 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3176 Do not enable ion/water position exchanges.
3178 .. mdp-value:: X ; Y ; Z
3180 Allow for ion/water position exchanges along the chosen direction.
3181 In a typical setup with the membranes parallel to the x-y plane,
3182 ion/water pairs need to be exchanged in Z direction to sustain the
3183 requested ion concentrations in the compartments.
3185 .. mdp:: swap-frequency
3187 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3188 per compartment are determined and exchanges made if necessary.
3189 Normally it is not necessary to check at every time step.
3190 For typical Computational Electrophysiology setups, a value of about 100 is
3191 sufficient and yields a negligible performance impact.
3193 .. mdp:: split-group0
3195 Name of the index group of the membrane-embedded part of channel #0.
3196 The center of mass of these atoms defines one of the compartment boundaries
3197 and should be chosen such that it is near the center of the membrane.
3199 .. mdp:: split-group1
3201 Channel #1 defines the position of the other compartment boundary.
3203 .. mdp:: massw-split0
3205 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3209 Use the geometrical center.
3213 Use the center of mass.
3215 .. mdp:: massw-split1
3217 (no) As above, but for split-group #1.
3219 .. mdp:: solvent-group
3221 Name of the index group of solvent molecules.
3223 .. mdp:: coupl-steps
3225 (10) Average the number of ions per compartment over these many swap attempt steps.
3226 This can be used to prevent that ions near a compartment boundary
3227 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3231 (1) The number of different ion types to be controlled. These are during the
3232 simulation exchanged with solvent molecules to reach the desired reference numbers.
3234 .. mdp:: iontype0-name
3236 Name of the first ion type.
3238 .. mdp:: iontype0-in-A
3240 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3241 The default value of -1 means: use the number of ions as found in time step 0
3244 .. mdp:: iontype0-in-B
3246 (-1) Reference number of ions of type 0 for compartment B.
3248 .. mdp:: bulk-offsetA
3250 (0.0) Offset of the first swap layer from the compartment A midplane.
3251 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3252 at maximum distance (= bulk concentration) to the split group layers. However,
3253 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3254 towards one of the compartment-partitioning layers (at +/- 1.0).
3256 .. mdp:: bulk-offsetB
3258 (0.0) Offset of the other swap layer from the compartment B midplane.
3263 (\1) Only swap ions if threshold difference to requested count is reached.
3267 (2.0) [nm] Radius of the split cylinder #0.
3268 Two split cylinders (mimicking the channel pores) can optionally be defined
3269 relative to the center of the split group. With the help of these cylinders
3270 it can be counted which ions have passed which channel. The split cylinder
3271 definition has no impact on whether or not ion/water swaps are done.
3275 (1.0) [nm] Upper extension of the split cylinder #0.
3279 (1.0) [nm] Lower extension of the split cylinder #0.
3283 (2.0) [nm] Radius of the split cylinder #1.
3287 (1.0) [nm] Upper extension of the split cylinder #1.
3291 (1.0) [nm] Lower extension of the split cylinder #1.
3294 User defined thingies
3295 ^^^^^^^^^^^^^^^^^^^^^
3299 .. mdp:: userint1 (0)
3300 .. mdp:: userint2 (0)
3301 .. mdp:: userint3 (0)
3302 .. mdp:: userint4 (0)
3303 .. mdp:: userreal1 (0)
3304 .. mdp:: userreal2 (0)
3305 .. mdp:: userreal3 (0)
3306 .. mdp:: userreal4 (0)
3308 These you can use if you modify code. You can pass integers and
3309 reals and groups to your subroutine. Check the inputrec definition
3310 in ``src/gromacs/mdtypes/inputrec.h``
3315 These features have been removed from |Gromacs|, but so that old
3316 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3317 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3318 fatal error if this is set.
3324 .. mdp:: implicit-solvent
3328 .. _reference manual: gmx-manual-parent-dir_