2 See the "run control" section for a working example of the
3 syntax to use when making .mdp entries, with and without detailed
4 documentation for values those entries might take. Everything can
5 be cross-referenced, see the examples there. TODO Make more
8 Molecular dynamics parameters (.mdp options)
9 ============================================
14 Default values are given in parentheses, or listed first among
15 choices. The first option in the list is always the default
16 option. Units are given in square brackets. The difference between a
17 dash and an underscore is ignored.
19 A :ref:`sample mdp file <mdp>` is available. This should be
20 appropriate to start a normal simulation. Edit it to suit your
21 specific needs and desires.
29 directories to include in your topology. Format:
30 ``-I/home/john/mylib -I../otherlib``
34 defines to pass to the preprocessor, default is no defines. You can
35 use any defines to control options in your customized topology
36 files. Options that act on existing :ref:`top` file mechanisms
39 ``-DFLEXIBLE`` will use flexible water instead of rigid water
40 into your topology, this can be useful for normal mode analysis.
42 ``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
43 your topology, used for implementing position restraints.
51 (Despite the name, this list includes algorithms that are not
52 actually integrators over time. :mdp-value:`integrator=steep` and
53 all entries following it are in this category)
57 A leap-frog algorithm for integrating Newton's equations of motion.
61 A velocity Verlet algorithm for integrating Newton's equations
62 of motion. For constant NVE simulations started from
63 corresponding points in the same trajectory, the trajectories
64 are analytically, but not binary, identical to the
65 :mdp-value:`integrator=md` leap-frog integrator. The the kinetic
66 energy, which is determined from the whole step velocities and
67 is therefore slightly too high. The advantage of this integrator
68 is more accurate, reversible Nose-Hoover and Parrinello-Rahman
69 coupling integration based on Trotter expansion, as well as
70 (slightly too small) full step velocity output. This all comes
71 at the cost off extra computation, especially with constraints
72 and extra communication in parallel. Note that for nearly all
73 production simulations the :mdp-value:`integrator=md` integrator
76 .. mdp-value:: md-vv-avek
78 A velocity Verlet algorithm identical to
79 :mdp-value:`integrator=md-vv`, except that the kinetic energy is
80 determined as the average of the two half step kinetic energies
81 as in the :mdp-value:`integrator=md` integrator, and this thus
82 more accurate. With Nose-Hoover and/or Parrinello-Rahman
83 coupling this comes with a slight increase in computational
88 An accurate and efficient leap-frog stochastic dynamics
89 integrator. With constraints, coordinates needs to be
90 constrained twice per integration step. Depending on the
91 computational cost of the force calculation, this can take a
92 significant part of the simulation time. The temperature for one
93 or more groups of atoms (:mdp:`tc-grps`) is set with
94 :mdp:`ref-t`, the inverse friction constant for each group is
95 set with :mdp:`tau-t`. The parameter :mdp:`tcoupl` is
96 ignored. The random generator is initialized with
97 :mdp:`ld-seed`. When used as a thermostat, an appropriate value
98 for :mdp:`tau-t` is 2 ps, since this results in a friction that
99 is lower than the internal friction of water, while it is high
100 enough to remove excess heat NOTE: temperature deviations decay
101 twice as fast as with a Berendsen thermostat with the same
106 An Euler integrator for Brownian or position Langevin dynamics,
107 the velocity is the force divided by a friction coefficient
108 (:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
109 :mdp:`bd-fric` is 0, the friction coefficient for each particle
110 is calculated as mass/ :mdp:`tau-t`, as for the integrator
111 :mdp-value:`integrator=sd`. The random generator is initialized
116 A steepest descent algorithm for energy minimization. The
117 maximum step size is :mdp:`emstep`, the tolerance is
122 A conjugate gradient algorithm for energy minimization, the
123 tolerance is :mdp:`emtol`. CG is more efficient when a steepest
124 descent step is done every once in a while, this is determined
125 by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
126 analysis, which requires a very high accuracy, |Gromacs| should be
127 compiled in double precision.
129 .. mdp-value:: l-bfgs
131 A quasi-Newtonian algorithm for energy minimization according to
132 the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
133 practice this seems to converge faster than Conjugate Gradients,
134 but due to the correction steps necessary it is not (yet)
139 Normal mode analysis is performed on the structure in the :ref:`tpr`
140 file. |Gromacs| should be compiled in double precision.
144 Test particle insertion. The last molecule in the topology is
145 the test particle. A trajectory must be provided to ``mdrun
146 -rerun``. This trajectory should not contain the molecule to be
147 inserted. Insertions are performed :mdp:`nsteps` times in each
148 frame at random locations and with random orientiations of the
149 molecule. When :mdp:`nstlist` is larger than one,
150 :mdp:`nstlist` insertions are performed in a sphere with radius
151 :mdp:`rtpi` around a the same random location using the same
152 neighborlist. Since neighborlist construction is expensive,
153 one can perform several extra insertions with the same list
154 almost for free. The random seed is set with
155 :mdp:`ld-seed`. The temperature for the Boltzmann weighting is
156 set with :mdp:`ref-t`, this should match the temperature of the
157 simulation of the original trajectory. Dispersion correction is
158 implemented correctly for TPI. All relevant quantities are
159 written to the file specified with ``mdrun -tpi``. The
160 distribution of insertion energies is written to the file
161 specified with ``mdrun -tpid``. No trajectory or energy file is
162 written. Parallel TPI gives identical results to single-node
163 TPI. For charged molecules, using PME with a fine grid is most
164 accurate and also efficient, since the potential in the system
165 only needs to be calculated once per frame.
169 Test particle insertion into a predefined cavity location. The
170 procedure is the same as for :mdp-value:`integrator=tpi`, except
171 that one coordinate extra is read from the trajectory, which is
172 used as the insertion location. The molecule to be inserted
173 should be centered at 0,0,0. |Gromacs| does not do this for you,
174 since for different situations a different way of centering
175 might be optimal. Also :mdp:`rtpi` sets the radius for the
176 sphere around this location. Neighbor searching is done only
177 once per frame, :mdp:`nstlist` is not used. Parallel
178 :mdp-value:`integrator=tpic` gives identical results to
179 single-rank :mdp-value:`integrator=tpic`.
184 starting time for your run (only makes sense for time-based
190 time step for integration (only makes sense for time-based
196 maximum number of steps to integrate or minimize, -1 is no
202 The starting step. The time at an step i in a run is
203 calculated as: t = :mdp:`tinit` + :mdp:`dt` *
204 (:mdp:`init-step` + i). The free-energy lambda is calculated
205 as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
206 (:mdp:`init-step` + i). Also non-equilibrium MD parameters can
207 depend on the step number. Thus for exact restarts or redoing
208 part of a run it might be necessary to set :mdp:`init-step` to
209 the step number of the restart frame. :ref:`gmx convert-tpr`
210 does this automatically.
212 .. mdp:: simulation-part
215 A simulation can consist of multiple parts, each of which has
216 a part number. This option specifies what that number will
217 be, which helps keep track of parts that are logically the
218 same simulation. This option is generally useful to set only
219 when coping with a crashed simulation where files were lost.
223 .. mdp-value:: Linear
225 Remove center of mass translational velocity
227 .. mdp-value:: Angular
229 Remove center of mass translational and rotational velocity around
232 .. mdp-value:: Linear-acceleration-correction
234 Remove center of mass translational velocity. Correct the center of
235 mass position assuming linear acceleration over :mdp:`nstcomm` steps.
236 This is useful for cases where an acceleration is expected on the
237 center of mass which is nearly constant over mdp:`nstcomm` steps.
238 This can occur for example when pulling on a group using an absolute
243 No restriction on the center of mass motion
248 frequency for center of mass motion removal
252 group(s) for center of mass motion removal, default is the whole
262 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
263 the friction coefficient for each particle is calculated as mass/
269 used to initialize random generator for thermal noise for
270 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
271 a pseudo random seed is used. When running BD or SD on multiple
272 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
273 the processor number.
281 (10.0) \[kJ mol-1 nm-1\]
282 the minimization is converged when the maximum force is smaller
293 frequency of performing 1 steepest descent step while doing
294 conjugate gradient energy minimization.
299 Number of correction steps to use for L-BFGS minimization. A higher
300 number is (at least theoretically) more accurate, but slower.
303 Shell Molecular Dynamics
304 ^^^^^^^^^^^^^^^^^^^^^^^^
306 When shells or flexible constraints are present in the system the
307 positions of the shells and the lengths of the flexible constraints
308 are optimized at every time step until either the RMS force on the
309 shells and constraints is less than :mdp:`emtol`, or a maximum number
310 of iterations :mdp:`niter` has been reached. Minimization is converged
311 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
312 value should be 1.0 at most.
317 maximum number of iterations for optimizing the shell positions and
318 the flexible constraints.
323 the step size for optimizing the flexible constraints. Should be
324 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
325 particles in a flexible constraint and d2V/dq2 is the second
326 derivative of the potential in the constraint direction. Hopefully
327 this number does not differ too much between the flexible
328 constraints, as the number of iterations and thus the runtime is
329 very sensitive to fcstep. Try several values!
332 Test particle insertion
333 ^^^^^^^^^^^^^^^^^^^^^^^
338 the test particle insertion radius, see integrators
339 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
348 number of steps that elapse between writing coordinates to output
349 trajectory file, the last coordinates are always written
354 number of steps that elapse between writing velocities to output
355 trajectory, the last velocities are always written
360 number of steps that elapse between writing forces to output
366 number of steps that elapse between writing energies to the log
367 file, the last energies are always written
369 .. mdp:: nstcalcenergy
372 number of steps that elapse between calculating the energies, 0 is
373 never. This option is only relevant with dynamics. This option affects the
374 performance in parallel simulations, because calculating energies
375 requires global communication between all processes which can
376 become a bottleneck at high parallelization.
381 number of steps that else between writing energies to energy file,
382 the last energies are always written, should be a multiple of
383 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
384 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
385 energy file, so :ref:`gmx energy` can report exact energy averages
386 and fluctuations also when :mdp:`nstenergy` > 1
388 .. mdp:: nstxout-compressed
391 number of steps that elapse between writing position coordinates
392 using lossy compression
394 .. mdp:: compressed-x-precision
397 precision with which to write to the compressed trajectory file
399 .. mdp:: compressed-x-grps
401 group(s) to write to the compressed trajectory file, by default the
402 whole system is written (if :mdp:`nstxout-compressed` > 0)
406 group(s) for which to write to write short-ranged non-bonded
407 potential energies to the energy file (not supported on GPUs)
413 .. mdp:: cutoff-scheme
415 .. mdp-value:: Verlet
417 Generate a pair list with buffering. The buffer size is
418 automatically set based on :mdp:`verlet-buffer-tolerance`,
419 unless this is set to -1, in which case :mdp:`rlist` will be
420 used. This option has an explicit, exact cut-off at :mdp:`rvdw`
421 equal to :mdp:`rcoulomb`, unless PME or Ewald is used, in which
422 case :mdp:`rcoulomb` > :mdp:`rvdw` is allowed. Currently only
423 cut-off, reaction-field, PME or Ewald electrostatics and plain
424 LJ are supported. Some :ref:`gmx mdrun` functionality is not yet
425 supported with the :mdp:`Verlet` scheme, but :ref:`gmx grompp`
426 checks for this. Native GPU acceleration is only supported with
427 :mdp:`Verlet`. With GPU-accelerated PME or with separate PME
428 ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
429 balance by scaling :mdp:`rcoulomb` and the grid spacing. This
430 can be turned off with ``mdrun -notunepme``. :mdp:`Verlet` is
431 faster than :mdp:`group` when there is no water, or if
432 :mdp:`group` would use a pair-list buffer to conserve energy.
436 Generate a pair list for groups of atoms. These groups
437 correspond to the charge groups in the topology. This was the
438 only cut-off treatment scheme before version 4.6, and is
439 **deprecated in |gmx-version|**. There is no explicit buffering of
440 the pair list. This enables efficient force calculations for
441 water, but energy is only conserved when a buffer is explicitly
450 Frequency to update the neighbor list. When this is 0, the
451 neighbor list is made only once. With energy minimization the
452 neighborlist will be updated for every energy evaluation when
453 :mdp:`nstlist` is greater than 0. With :mdp:`Verlet` and
454 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
455 a minimum value and :ref:`gmx mdrun` might increase it, unless
456 it is set to 1. With parallel simulations and/or non-bonded
457 force calculation on the GPU, a value of 20 or 40 often gives
458 the best performance. With :mdp:`group` and non-exact
459 cut-off's, :mdp:`nstlist` will affect the accuracy of your
460 simulation and it can not be chosen freely.
464 The neighbor list is only constructed once and never
465 updated. This is mainly useful for vacuum simulations in which
466 all particles see each other.
476 Make a grid in the box and only check atoms in neighboring grid
477 cells when constructing a new neighbor list every
478 :mdp:`nstlist` steps. In large systems grid search is much
479 faster than simple search.
481 .. mdp-value:: simple
483 Check every atom in the box when constructing a new neighbor
484 list every :mdp:`nstlist` steps (only with :mdp:`group`
491 Use periodic boundary conditions in all directions.
495 Use no periodic boundary conditions, ignore the box. To simulate
496 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
497 best performance without cut-offs on a single MPI rank, set
498 :mdp:`nstlist` to zero and :mdp:`ns-type` =simple.
502 Use periodic boundary conditions in x and y directions
503 only. This works only with :mdp:`ns-type` =grid and can be used
504 in combination with walls_. Without walls or with only one wall
505 the system size is infinite in the z direction. Therefore
506 pressure coupling or Ewald summation methods can not be
507 used. These disadvantages do not apply when two walls are used.
509 .. mdp:: periodic-molecules
513 molecules are finite, fast molecular PBC can be used
517 for systems with molecules that couple to themselves through the
518 periodic boundary conditions, this requires a slower PBC
519 algorithm and molecules are not made whole in the output
521 .. mdp:: verlet-buffer-tolerance
523 (0.005) \[kJ/mol/ps\]
525 Useful only with the :mdp:`Verlet` :mdp:`cutoff-scheme`. This sets
526 the maximum allowed error for pair interactions per particle caused
527 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
528 :mdp:`nstlist` and the Verlet buffer size are fixed (for
529 performance reasons), particle pairs not in the pair list can
530 occasionally get within the cut-off distance during
531 :mdp:`nstlist` -1 steps. This causes very small jumps in the
532 energy. In a constant-temperature ensemble, these very small energy
533 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
534 estimate assumes a homogeneous particle distribution, hence the
535 errors might be slightly underestimated for multi-phase
536 systems. (See the `reference manual`_ for details). For longer
537 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
538 overestimated, because the interactions between particles are
539 ignored. Combined with cancellation of errors, the actual drift of
540 the total energy is usually one to two orders of magnitude
541 smaller. Note that the generated buffer size takes into account
542 that the |Gromacs| pair-list setup leads to a reduction in the
543 drift by a factor 10, compared to a simple particle-pair based
544 list. Without dynamics (energy minimization etc.), the buffer is 5%
545 of the cut-off. For NVE simulations the initial temperature is
546 used, unless this is zero, in which case a buffer of 10% is
547 used. For NVE simulations the tolerance usually needs to be lowered
548 to achieve proper energy conservation on the nanosecond time
549 scale. To override the automated buffer setting, use
550 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
555 Cut-off distance for the short-range neighbor list. With the
556 :mdp:`Verlet` :mdp:`cutoff-scheme`, this is by default set by the
557 :mdp:`verlet-buffer-tolerance` option and the value of
558 :mdp:`rlist` is ignored.
566 .. mdp-value:: Cut-off
568 Plain cut-off with neighborlist radius :mdp:`rlist` and
569 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
574 Classical Ewald sum electrostatics. The real-space cut-off
575 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
576 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
577 of wave vectors used in reciprocal space is controlled by
578 :mdp:`fourierspacing`. The relative accuracy of
579 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
581 NOTE: Ewald scales as O(N^3/2) and is thus extremely slow for
582 large systems. It is included mainly for reference - in most
583 cases PME will perform much better.
587 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
588 space is similar to the Ewald sum, while the reciprocal part is
589 performed with FFTs. Grid dimensions are controlled with
590 :mdp:`fourierspacing` and the interpolation order with
591 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
592 interpolation the electrostatic forces have an accuracy of
593 2-3*10^-4. Since the error from the vdw-cutoff is larger than
594 this you might try 0.15 nm. When running in parallel the
595 interpolation parallelizes better than the FFT, so try
596 decreasing grid dimensions while increasing interpolation.
598 .. mdp-value:: P3M-AD
600 Particle-Particle Particle-Mesh algorithm with analytical
601 derivative for for long range electrostatic interactions. The
602 method and code is identical to SPME, except that the influence
603 function is optimized for the grid. This gives a slight increase
606 .. mdp-value:: Reaction-Field
608 Reaction field electrostatics with Coulomb cut-off
609 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
610 dielectric constant beyond the cut-off is
611 :mdp:`epsilon-rf`. The dielectric constant can be set to
612 infinity by setting :mdp:`epsilon-rf` =0.
614 .. mdp-value:: Generalized-Reaction-Field
616 Generalized reaction field with Coulomb cut-off
617 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rcoulomb`. The
618 dielectric constant beyond the cut-off is
619 :mdp:`epsilon-rf`. The ionic strength is computed from the
620 number of charged (*i.e.* with non zero charge) charge
621 groups. The temperature for the GRF potential is set with
624 .. mdp-value:: Reaction-Field-zero
626 In |Gromacs|, normal reaction-field electrostatics with
627 :mdp:`cutoff-scheme` = :mdp:`group` leads to bad energy
628 conservation. :mdp:`Reaction-Field-zero` solves this by making
629 the potential zero beyond the cut-off. It can only be used with
630 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
631 only for that value the force vanishes at the
632 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
633 :mdp:`rcoulomb` to accommodate for the size of charge groups
634 and diffusion between neighbor list updates. This, and the fact
635 that table lookups are used instead of analytical functions make
636 :mdp:`Reaction-Field-zero` computationally more expensive than
637 normal reaction-field.
641 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
642 might want to use :mdp:`Reaction-Field-zero` instead, which has
643 a similar potential shape, but has a physical interpretation and
644 has better energies due to the exclusion correction terms.
646 .. mdp-value:: Encad-Shift
648 The Coulomb potential is decreased over the whole range, using
649 the definition from the Encad simulation package.
651 .. mdp-value:: Switch
653 Analogous to :mdp-value:`vdwtype=Switch` for
654 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
655 serious artifacts, advice: use :mdp:`Reaction-Field-zero`
660 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
661 with user-defined potential functions for repulsion, dispersion
662 and Coulomb. When pair interactions are present, :ref:`gmx
663 mdrun` also expects to find a file ``tablep.xvg`` for the pair
664 interactions. When the same interactions should be used for
665 non-bonded and pair interactions the user can specify the same
666 file name for both table files. These files should contain 7
667 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
668 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
669 function, ``g(x)`` the dispersion function and ``h(x)`` the
670 repulsion function. When :mdp:`vdwtype` is not set to User the
671 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
672 the non-bonded interactions ``x`` values should run from 0 to
673 the largest cut-off distance + :mdp:`table-extension` and
674 should be uniformly spaced. For the pair interactions the table
675 length in the file will be used. The optimal spacing, which is
676 used for non-user tables, is ``0.002 nm`` when you run in mixed
677 precision or ``0.0005 nm`` when you run in double precision. The
678 function value at ``x=0`` is not important. More information is
679 in the printed manual.
681 .. mdp-value:: PME-Switch
683 A combination of PME and a switch function for the direct-space
684 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
685 :mdp:`rlist`. This is mainly useful constant energy simulations
686 (note that using PME with :mdp:`cutoff-scheme` = :mdp:`Verlet`
687 will be more efficient).
689 .. mdp-value:: PME-User
691 A combination of PME and user tables (see
692 above). :mdp:`rcoulomb` is allowed to be smaller than
693 :mdp:`rlist`. The PME mesh contribution is subtracted from the
694 user table by :ref:`gmx mdrun`. Because of this subtraction the
695 user tables should contain about 10 decimal places.
697 .. mdp-value:: PME-User-Switch
699 A combination of PME-User and a switching function (see
700 above). The switching function is applied to final
701 particle-particle interaction, *i.e.* both to the user supplied
702 function and the PME Mesh correction part.
704 .. mdp:: coulomb-modifier
706 .. mdp-value:: Potential-shift-Verlet
708 Selects Potential-shift with the Verlet cutoff-scheme, as it is
709 (nearly) free; selects None with the group cutoff-scheme.
711 .. mdp-value:: Potential-shift
713 Shift the Coulomb potential by a constant such that it is zero
714 at the cut-off. This makes the potential the integral of the
715 force. Note that this does not affect the forces or the
720 Use an unmodified Coulomb potential. With the group scheme this
721 means no exact cut-off is used, energies and forces are
722 calculated for all pairs in the neighborlist.
724 .. mdp:: rcoulomb-switch
727 where to start switching the Coulomb potential, only relevant
728 when force or potential switching is used
733 distance for the Coulomb cut-off
738 The relative dielectric constant. A value of 0 means infinity.
743 The relative dielectric constant of the reaction field. This
744 is only used with reaction-field electrostatics. A value of 0
753 .. mdp-value:: Cut-off
755 Twin range cut-offs with neighbor list cut-off :mdp:`rlist` and
756 VdW cut-off :mdp:`rvdw`, where :mdp:`rvdw` >= :mdp:`rlist`.
760 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
761 grid dimensions are controlled with :mdp:`fourierspacing` in
762 the same way as for electrostatics, and the interpolation order
763 is controlled with :mdp:`pme-order`. The relative accuracy of
764 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
765 and the specific combination rules that are to be used by the
766 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
770 This functionality is deprecated and replaced by
771 :mdp:`vdw-modifier` = Force-switch. The LJ (not Buckingham)
772 potential is decreased over the whole range and the forces decay
773 smoothly to zero between :mdp:`rvdw-switch` and
774 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
775 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
776 size of charge groups and diffusion between neighbor list
779 .. mdp-value:: Switch
781 This functionality is deprecated and replaced by
782 :mdp:`vdw-modifier` = Potential-switch. The LJ (not Buckingham)
783 potential is normal out to :mdp:`rvdw-switch`, after which it
784 is switched off to reach zero at :mdp:`rvdw`. Both the
785 potential and force functions are continuously smooth, but be
786 aware that all switch functions will give rise to a bulge
787 (increase) in the force (since we are switching the
788 potential). The neighbor search cut-off :mdp:`rlist` should be
789 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
790 size of charge groups and diffusion between neighbor list
793 .. mdp-value:: Encad-Shift
795 The LJ (not Buckingham) potential is decreased over the whole
796 range, using the definition from the Encad simulation package.
800 See user for :mdp:`coulombtype`. The function value at zero is
801 not important. When you want to use LJ correction, make sure
802 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
803 function. When :mdp:`coulombtype` is not set to User the values
804 for the ``f`` and ``-f'`` columns are ignored.
806 .. mdp:: vdw-modifier
808 .. mdp-value:: Potential-shift-Verlet
810 Selects Potential-shift with the Verlet cutoff-scheme, as it is
811 (nearly) free; selects None with the group cutoff-scheme.
813 .. mdp-value:: Potential-shift
815 Shift the Van der Waals potential by a constant such that it is
816 zero at the cut-off. This makes the potential the integral of
817 the force. Note that this does not affect the forces or the
822 Use an unmodified Van der Waals potential. With the group scheme
823 this means no exact cut-off is used, energies and forces are
824 calculated for all pairs in the neighborlist.
826 .. mdp-value:: Force-switch
828 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
829 and :mdp:`rvdw`. This shifts the potential shift over the whole
830 range and switches it to zero at the cut-off. Note that this is
831 more expensive to calculate than a plain cut-off and it is not
832 required for energy conservation, since Potential-shift
833 conserves energy just as well.
835 .. mdp-value:: Potential-switch
837 Smoothly switches the potential to zero between
838 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
839 articifically large forces in the switching region and is much
840 more expensive to calculate. This option should only be used if
841 the force field you are using requires this.
847 where to start switching the LJ force and possibly the potential,
848 only relevant when force or potential switching is used
853 distance for the LJ or Buckingham cut-off
859 don't apply any correction
861 .. mdp-value:: EnerPres
863 apply long range dispersion corrections for Energy and Pressure
867 apply long range dispersion corrections for Energy only
873 .. mdp:: table-extension
876 Extension of the non-bonded potential lookup tables beyond the
877 largest cut-off distance. The value should be large enough to
878 account for charge group sizes and the diffusion between
879 neighbor-list updates. Without user defined potential the same
880 table length is used for the lookup tables for the 1-4
881 interactions, which are always tabulated irrespective of the use of
882 tables for the non-bonded interactions. The value of
883 :mdp:`table-extension` in no way affects the values of
884 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
886 .. mdp:: energygrp-table
888 When user tables are used for electrostatics and/or VdW, here one
889 can give pairs of energy groups for which seperate user tables
890 should be used. The two energy groups will be appended to the table
891 file name, in order of their definition in :mdp:`energygrps`,
892 seperated by underscores. For example, if ``energygrps = Na Cl
893 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
894 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
895 normal ``table.xvg`` which will be used for all other energy group
902 .. mdp:: fourierspacing
905 For ordinary Ewald, the ratio of the box dimensions and the spacing
906 determines a lower bound for the number of wave vectors to use in
907 each (signed) direction. For PME and P3M, that ratio determines a
908 lower bound for the number of Fourier-space grid points that will
909 be used along that axis. In all cases, the number for each
910 direction can be overridden by entering a non-zero value for that
911 :mdp:`fourier-nx` direction. For optimizing the relative load of
912 the particle-particle interactions and the mesh part of PME, it is
913 useful to know that the accuracy of the electrostatics remains
914 nearly constant when the Coulomb cut-off and the PME grid spacing
915 are scaled by the same factor.
922 Highest magnitude of wave vectors in reciprocal space when using Ewald.
923 Grid size when using PME or P3M. These values override
924 :mdp:`fourierspacing` per direction. The best choice is powers of
925 2, 3, 5 and 7. Avoid large primes.
930 Interpolation order for PME. 4 equals cubic interpolation. You
931 might try 6/8/10 when running in parallel and simultaneously
932 decrease grid dimension.
937 The relative strength of the Ewald-shifted direct potential at
938 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
939 will give a more accurate direct sum, but then you need more wave
940 vectors for the reciprocal sum.
942 .. mdp:: ewald-rtol-lj
945 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
946 to control the relative strength of the dispersion potential at
947 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
948 electrostatic potential.
950 .. mdp:: lj-pme-comb-rule
953 The combination rules used to combine VdW-parameters in the
954 reciprocal part of LJ-PME. Geometric rules are much faster than
955 Lorentz-Berthelot and usually the recommended choice, even when the
956 rest of the force field uses the Lorentz-Berthelot rules.
958 .. mdp-value:: Geometric
960 Apply geometric combination rules
962 .. mdp-value:: Lorentz-Berthelot
964 Apply Lorentz-Berthelot combination rules
966 .. mdp:: ewald-geometry
970 The Ewald sum is performed in all three dimensions.
974 The reciprocal sum is still performed in 3D, but a force and
975 potential correction applied in the `z` dimension to produce a
976 pseudo-2D summation. If your system has a slab geometry in the
977 `x-y` plane you can try to increase the `z`-dimension of the box
978 (a box height of 3 times the slab height is usually ok) and use
981 .. mdp:: epsilon-surface
984 This controls the dipole correction to the Ewald summation in
985 3D. The default value of zero means it is turned off. Turn it on by
986 setting it to the value of the relative permittivity of the
987 imaginary surface around your infinite system. Be careful - you
988 shouldn't use this if you have free mobile charges in your
989 system. This value does not affect the slab 3DC variant of the long
1000 No temperature coupling.
1002 .. mdp-value:: berendsen
1004 Temperature coupling with a Berendsen-thermostat to a bath with
1005 temperature :mdp:`ref-t`, with time constant
1006 :mdp:`tau-t`. Several groups can be coupled separately, these
1007 are specified in the :mdp:`tc-grps` field separated by spaces.
1009 .. mdp-value:: nose-hoover
1011 Temperature coupling using a Nose-Hoover extended ensemble. The
1012 reference temperature and coupling groups are selected as above,
1013 but in this case :mdp:`tau-t` controls the period of the
1014 temperature fluctuations at equilibrium, which is slightly
1015 different from a relaxation time. For NVT simulations the
1016 conserved energy quantity is written to energy and log file.
1018 .. mdp-value:: andersen
1020 Temperature coupling by randomizing a fraction of the particles
1021 at each timestep. Reference temperature and coupling groups are
1022 selected as above. :mdp:`tau-t` is the average time between
1023 randomization of each molecule. Inhibits particle dynamics
1024 somewhat, but little or no ergodicity issues. Currently only
1025 implemented with velocity Verlet, and not implemented with
1028 .. mdp-value:: andersen-massive
1030 Temperature coupling by randomizing all particles at infrequent
1031 timesteps. Reference temperature and coupling groups are
1032 selected as above. :mdp:`tau-t` is the time between
1033 randomization of all molecules. Inhibits particle dynamics
1034 somewhat, but little or no ergodicity issues. Currently only
1035 implemented with velocity Verlet.
1037 .. mdp-value:: v-rescale
1039 Temperature coupling using velocity rescaling with a stochastic
1040 term (JCP 126, 014101). This thermostat is similar to Berendsen
1041 coupling, with the same scaling using :mdp:`tau-t`, but the
1042 stochastic term ensures that a proper canonical ensemble is
1043 generated. The random seed is set with :mdp:`ld-seed`. This
1044 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1045 simulations the conserved energy quantity is written to the
1046 energy and log file.
1051 The frequency for coupling the temperature. The default value of -1
1052 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1053 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1054 Verlet integrators :mdp:`nsttcouple` is set to 1.
1056 .. mdp:: nh-chain-length
1059 The number of chained Nose-Hoover thermostats for velocity Verlet
1060 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1061 only supports 1. Data for the NH chain variables is not printed to
1062 the :ref:`edr` file, but can be using the ``GMX_NOSEHOOVER_CHAINS``
1063 environment variable
1067 groups to couple to separate temperature baths
1072 time constant for coupling (one for each group in
1073 :mdp:`tc-grps`), -1 means no temperature coupling
1078 reference temperature for coupling (one for each group in
1089 No pressure coupling. This means a fixed box size.
1091 .. mdp-value:: Berendsen
1093 Exponential relaxation pressure coupling with time constant
1094 :mdp:`tau-p`. The box is scaled every timestep. It has been
1095 argued that this does not yield a correct thermodynamic
1096 ensemble, but it is the most efficient way to scale a box at the
1099 .. mdp-value:: Parrinello-Rahman
1101 Extended-ensemble pressure coupling where the box vectors are
1102 subject to an equation of motion. The equation of motion for the
1103 atoms is coupled to this. No instantaneous scaling takes
1104 place. As for Nose-Hoover temperature coupling the time constant
1105 :mdp:`tau-p` is the period of pressure fluctuations at
1106 equilibrium. This is probably a better method when you want to
1107 apply pressure scaling during data collection, but beware that
1108 you can get very large oscillations if you are starting from a
1109 different pressure. For simulations where the exact fluctation
1110 of the NPT ensemble are important, or if the pressure coupling
1111 time is very short it may not be appropriate, as the previous
1112 time step pressure is used in some steps of the |Gromacs|
1113 implementation for the current time step pressure.
1117 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1118 :mdp-value:`md-vv` or :mdp-value:`md-vv-avek`, very similar to
1119 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1120 time constant :mdp:`tau-p` is the period of pressure
1121 fluctuations at equilibrium. This is probably a better method
1122 when you want to apply pressure scaling during data collection,
1123 but beware that you can get very large oscillations if you are
1124 starting from a different pressure. Currently (as of version
1125 5.1), it only supports isotropic scaling, and only works without
1130 Specifies the kind of isotropy of the pressure coupling used. Each
1131 kind takes one or more values for :mdp:`compressibility` and
1132 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1134 .. mdp-value:: isotropic
1136 Isotropic pressure coupling with time constant
1137 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1138 :mdp:`ref-p` is required.
1140 .. mdp-value:: semiisotropic
1142 Pressure coupling which is isotropic in the ``x`` and ``y``
1143 direction, but different in the ``z`` direction. This can be
1144 useful for membrane simulations. Two values each for
1145 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1146 ``x/y`` and ``z`` directions respectively.
1148 .. mdp-value:: anisotropic
1150 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1151 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1152 respectively. When the off-diagonal compressibilities are set to
1153 zero, a rectangular box will stay rectangular. Beware that
1154 anisotropic scaling can lead to extreme deformation of the
1157 .. mdp-value:: surface-tension
1159 Surface tension coupling for surfaces parallel to the
1160 xy-plane. Uses normal pressure coupling for the `z`-direction,
1161 while the surface tension is coupled to the `x/y` dimensions of
1162 the box. The first :mdp:`ref-p` value is the reference surface
1163 tension times the number of surfaces ``bar nm``, the second
1164 value is the reference `z`-pressure ``bar``. The two
1165 :mdp:`compressibility` values are the compressibility in the
1166 `x/y` and `z` direction respectively. The value for the
1167 `z`-compressibility should be reasonably accurate since it
1168 influences the convergence of the surface-tension, it can also
1169 be set to zero to have a box with constant height.
1174 The frequency for coupling the pressure. The default value of -1
1175 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1176 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1177 Verlet integrators :mdp:`nstpcouple` is set to 1.
1182 The time constant for pressure coupling (one value for all
1185 .. mdp:: compressibility
1188 The compressibility (NOTE: this is now really in bar^-1) For water at 1
1189 atm and 300 K the compressibility is 4.5e-5 bar^-1. The number of
1190 required values is implied by :mdp:`pcoupltype`.
1195 The reference pressure for coupling. The number of required values
1196 is implied by :mdp:`pcoupltype`.
1198 .. mdp:: refcoord-scaling
1202 The reference coordinates for position restraints are not
1203 modified. Note that with this option the virial and pressure
1204 will depend on the absolute positions of the reference
1209 The reference coordinates are scaled with the scaling matrix of
1210 the pressure coupling.
1214 Scale the center of mass of the reference coordinates with the
1215 scaling matrix of the pressure coupling. The vectors of each
1216 reference coordinate to the center of mass are not scaled. Only
1217 one COM is used, even when there are multiple molecules with
1218 position restraints. For calculating the COM of the reference
1219 coordinates in the starting configuration, periodic boundary
1220 conditions are not taken into account.
1226 Simulated annealing is controlled separately for each temperature
1227 group in |Gromacs|. The reference temperature is a piecewise linear
1228 function, but you can use an arbitrary number of points for each
1229 group, and choose either a single sequence or a periodic behaviour for
1230 each group. The actual annealing is performed by dynamically changing
1231 the reference temperature used in the thermostat algorithm selected,
1232 so remember that the system will usually not instantaneously reach the
1233 reference temperature!
1237 Type of annealing for each temperature group
1241 No simulated annealing - just couple to reference temperature value.
1243 .. mdp-value:: single
1245 A single sequence of annealing points. If your simulation is
1246 longer than the time of the last point, the temperature will be
1247 coupled to this constant value after the annealing sequence has
1248 reached the last time point.
1250 .. mdp-value:: periodic
1252 The annealing will start over at the first reference point once
1253 the last reference time is reached. This is repeated until the
1256 .. mdp:: annealing-npoints
1258 A list with the number of annealing reference/control points used
1259 for each temperature group. Use 0 for groups that are not
1260 annealed. The number of entries should equal the number of
1263 .. mdp:: annealing-time
1265 List of times at the annealing reference/control points for each
1266 group. If you are using periodic annealing, the times will be used
1267 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1268 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1269 etc. The number of entries should equal the sum of the numbers
1270 given in :mdp:`annealing-npoints`.
1272 .. mdp:: annealing-temp
1274 List of temperatures at the annealing reference/control points for
1275 each group. The number of entries should equal the sum of the
1276 numbers given in :mdp:`annealing-npoints`.
1278 Confused? OK, let's use an example. Assume you have two temperature
1279 groups, set the group selections to ``annealing = single periodic``,
1280 the number of points of each group to ``annealing-npoints = 3 4``, the
1281 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1282 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1283 will be coupled to 298K at 0ps, but the reference temperature will
1284 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1285 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1286 second group is coupled to 298K at 0ps, it increases linearly to 320K
1287 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1288 decreases to 298K, and then it starts over with the same pattern
1289 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1290 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1300 Do not generate velocities. The velocities are set to zero
1301 when there are no velocities in the input structure file.
1305 Generate velocities in :ref:`gmx grompp` according to a
1306 Maxwell distribution at temperature :mdp:`gen-temp`, with
1307 random seed :mdp:`gen-seed`. This is only meaningful with
1308 integrator :mdp-value:`integrator=md`.
1313 temperature for Maxwell distribution
1318 used to initialize random generator for random velocities,
1319 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1326 .. mdp:: constraints
1330 No constraints except for those defined explicitly in the
1331 topology, *i.e.* bonds are represented by a harmonic (or other)
1332 potential or a Morse potential (depending on the setting of
1333 :mdp:`morse`) and angles by a harmonic (or other) potential.
1335 .. mdp-value:: h-bonds
1337 Convert the bonds with H-atoms to constraints.
1339 .. mdp-value:: all-bonds
1341 Convert all bonds to constraints.
1343 .. mdp-value:: h-angles
1345 Convert all bonds and additionally the angles that involve
1346 H-atoms to bond-constraints.
1348 .. mdp-value:: all-angles
1350 Convert all bonds and angles to bond-constraints.
1352 .. mdp:: constraint-algorithm
1354 .. mdp-value:: LINCS
1356 LINear Constraint Solver. With domain decomposition the parallel
1357 version P-LINCS is used. The accuracy in set with
1358 :mdp:`lincs-order`, which sets the number of matrices in the
1359 expansion for the matrix inversion. After the matrix inversion
1360 correction the algorithm does an iterative correction to
1361 compensate for lengthening due to rotation. The number of such
1362 iterations can be controlled with :mdp:`lincs-iter`. The root
1363 mean square relative constraint deviation is printed to the log
1364 file every :mdp:`nstlog` steps. If a bond rotates more than
1365 :mdp:`lincs-warnangle` in one step, a warning will be printed
1366 both to the log file and to ``stderr``. LINCS should not be used
1367 with coupled angle constraints.
1369 .. mdp-value:: SHAKE
1371 SHAKE is slightly slower and less stable than LINCS, but does
1372 work with angle constraints. The relative tolerance is set with
1373 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1374 does not support constraints between atoms on different nodes,
1375 thus it can not be used with domain decompositon when inter
1376 charge-group constraints are present. SHAKE can not be used with
1377 energy minimization.
1379 .. mdp:: continuation
1381 This option was formerly known as unconstrained-start.
1385 apply constraints to the start configuration and reset shells
1389 do not apply constraints to the start configuration and do not
1390 reset shells, useful for exact coninuation and reruns
1395 relative tolerance for SHAKE
1397 .. mdp:: lincs-order
1400 Highest order in the expansion of the constraint coupling
1401 matrix. When constraints form triangles, an additional expansion of
1402 the same order is applied on top of the normal expansion only for
1403 the couplings within such triangles. For "normal" MD simulations an
1404 order of 4 usually suffices, 6 is needed for large time-steps with
1405 virtual sites or BD. For accurate energy minimization an order of 8
1406 or more might be required. With domain decomposition, the cell size
1407 is limited by the distance spanned by :mdp:`lincs-order` +1
1408 constraints. When one wants to scale further than this limit, one
1409 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1410 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1411 )* :mdp:`lincs-order` remains constant.
1416 Number of iterations to correct for rotational lengthening in
1417 LINCS. For normal runs a single step is sufficient, but for NVE
1418 runs where you want to conserve energy accurately or for accurate
1419 energy minimization you might want to increase it to 2.
1421 .. mdp:: lincs-warnangle
1424 maximum angle that a bond can rotate before LINCS will complain
1430 bonds are represented by a harmonic potential
1434 bonds are represented by a Morse potential
1437 Energy group exclusions
1438 ^^^^^^^^^^^^^^^^^^^^^^^
1440 .. mdp:: energygrp-excl
1442 Pairs of energy groups for which all non-bonded interactions are
1443 excluded. An example: if you have two energy groups ``Protein`` and
1444 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1445 would give only the non-bonded interactions between the protein and
1446 the solvent. This is especially useful for speeding up energy
1447 calculations with ``mdrun -rerun`` and for excluding interactions
1448 within frozen groups.
1457 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1458 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1459 ``=xy``. When set to 2 pressure coupling and Ewald summation can be
1460 used (it is usually best to use semiisotropic pressure coupling
1461 with the ``x/y`` compressibility set to 0, as otherwise the surface
1462 area will change). Walls interact wit the rest of the system
1463 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1464 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1465 monitor the interaction of energy groups with each wall. The center
1466 of mass motion removal will be turned off in the ``z``-direction.
1468 .. mdp:: wall-atomtype
1470 the atom type name in the force field for each wall. By (for
1471 example) defining a special wall atom type in the topology with its
1472 own combination rules, this allows for independent tuning of the
1473 interaction of each atomtype with the walls.
1479 LJ integrated over the volume behind the wall: 9-3 potential
1483 LJ integrated over the wall surface: 10-4 potential
1487 direct LJ potential with the ``z`` distance from the wall
1491 user defined potentials indexed with the ``z`` distance from the
1492 wall, the tables are read analogously to the
1493 :mdp:`energygrp-table` option, where the first name is for a
1494 "normal" energy group and the second name is ``wall0`` or
1495 ``wall1``, only the dispersion and repulsion columns are used
1497 .. mdp:: wall-r-linpot
1500 Below this distance from the wall the potential is continued
1501 linearly and thus the force is constant. Setting this option to a
1502 postive value is especially useful for equilibration when some
1503 atoms are beyond a wall. When the value is <=0 (<0 for
1504 :mdp:`wall-type` =table), a fatal error is generated when atoms
1507 .. mdp:: wall-density
1510 the number density of the atoms for each wall for wall types 9-3
1513 .. mdp:: wall-ewald-zfac
1516 The scaling factor for the third box vector for Ewald summation
1517 only, the minimum is 2. Ewald summation can only be used with
1518 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1519 ``=3dc``. The empty layer in the box serves to decrease the
1520 unphysical Coulomb interaction between periodic images.
1526 Note that where pulling coordinate are applicable, there can be more
1527 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1528 variables will exist accordingly. Documentation references to things
1529 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1530 applicable pulling coordinate.
1536 No center of mass pulling. All the following pull options will
1537 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1542 Center of mass pulling will be applied on 1 or more groups using
1543 1 or more pull coordinates.
1545 .. mdp:: pull-cylinder-r
1548 the radius of the cylinder for
1549 :mdp:`pull-coord1-geometry` = :mdp-value:`cylinder`
1551 .. mdp:: pull-constr-tol
1554 the relative constraint tolerance for constraint pulling
1556 .. mdp:: pull-print-com
1560 do not print the COM for any group
1564 print the COM of all groups for all pull coordinates
1566 .. mdp:: pull-print-ref-value
1570 do not print the reference value for each pull coordinate
1574 print the reference value for each pull coordinate
1576 .. mdp:: pull-print-components
1580 only print the distance for each pull coordinate
1584 print the distance and Cartesian components selected in
1585 :mdp:`pull-coord1-dim`
1587 .. mdp:: pull-nstxout
1590 frequency for writing out the COMs of all the pull group (0 is
1593 .. mdp:: pull-nstfout
1596 frequency for writing out the force of all the pulled group
1600 .. mdp:: pull-ngroups
1603 The number of pull groups, not including the absolute reference
1604 group, when used. Pull groups can be reused in multiple pull
1605 coordinates. Below only the pull options for group 1 are given,
1606 further groups simply increase the group index number.
1608 .. mdp:: pull-ncoords
1611 The number of pull coordinates. Below only the pull options for
1612 coordinate 1 are given, further coordinates simply increase the
1613 coordinate index number.
1615 .. mdp:: pull-group1-name
1617 The name of the pull group, is looked up in the index file or in
1618 the default groups to obtain the atoms involved.
1620 .. mdp:: pull-group1-weights
1622 Optional relative weights which are multiplied with the masses of
1623 the atoms to give the total weight for the COM. The number should
1624 be 0, meaning all 1, or the number of atoms in the pull group.
1626 .. mdp:: pull-group1-pbcatom
1629 The reference atom for the treatment of periodic boundary
1630 conditions inside the group (this has no effect on the treatment of
1631 the pbc between groups). This option is only important when the
1632 diameter of the pull group is larger than half the shortest box
1633 vector. For determining the COM, all atoms in the group are put at
1634 their periodic image which is closest to
1635 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1636 atom (number wise) is used. This parameter is not used with
1637 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1638 weighting, which is useful for a group of molecules in a periodic
1639 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1642 .. mdp:: pull-coord1-type
1644 .. mdp-value:: umbrella
1646 Center of mass pulling using an umbrella potential between the
1647 reference group and one or more groups.
1649 .. mdp-value:: constraint
1651 Center of mass pulling using a constraint between the reference
1652 group and one or more groups. The setup is identical to the
1653 option umbrella, except for the fact that a rigid constraint is
1654 applied instead of a harmonic potential.
1656 .. mdp-value:: constant-force
1658 Center of mass pulling using a linear potential and therefore a
1659 constant force. For this option there is no reference position
1660 and therefore the parameters :mdp:`pull-coord1-init` and
1661 :mdp:`pull-coord1-rate` are not used.
1663 .. mdp-value:: flat-bottom
1665 At distances above :mdp:`pull-coord1-init` a harmonic potential
1666 is applied, otherwise no potential is applied.
1668 .. mdp-value:: flat-bottom-high
1670 At distances below :mdp:`pull-coord1-init` a harmonic potential
1671 is applied, otherwise no potential is applied.
1673 .. mdp-value:: external-potential
1675 An external potential that needs to be provided by another
1678 .. mdp:: pull-coord1-potential-provider
1680 The name of the external module that provides the potential for
1681 the case where :mdp:`pull-coord1-type` is external-potential.
1683 .. mdp:: pull-coord1-geometry
1685 .. mdp-value:: distance
1687 Pull along the vector connecting the two groups. Components can
1688 be selected with :mdp:`pull-coord1-dim`.
1690 .. mdp-value:: direction
1692 Pull in the direction of :mdp:`pull-coord1-vec`.
1694 .. mdp-value:: direction-periodic
1696 As :mdp-value:`direction`, but allows the distance to be larger
1697 than half the box size. With this geometry the box should not be
1698 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1699 the pull force is not added to virial.
1701 .. mdp-value:: direction-relative
1703 As :mdp-value:`direction`, but the pull vector is the vector
1704 that points from the COM of a third to the COM of a fourth pull
1705 group. This means that 4 groups need to be supplied in
1706 :mdp:`pull-coord1-groups`. Note that the pull force will give
1707 rise to a torque on the pull vector, which is turn leads to
1708 forces perpendicular to the pull vector on the two groups
1709 defining the vector. If you want a pull group to move between
1710 the two groups defining the vector, simply use the union of
1711 these two groups as the reference group.
1713 .. mdp-value:: cylinder
1715 Designed for pulling with respect to a layer where the reference
1716 COM is given by a local cylindrical part of the reference group.
1717 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1718 the first of the two groups in :mdp:`pull-coord1-groups` a
1719 cylinder is selected around the axis going through the COM of
1720 the second group with direction :mdp:`pull-coord1-vec` with
1721 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1722 continously to zero as the radial distance goes from 0 to
1723 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1724 dependence gives rise to radial forces on both pull groups.
1725 Note that the radius should be smaller than half the box size.
1726 For tilted cylinders they should be even smaller than half the
1727 box size since the distance of an atom in the reference group
1728 from the COM of the pull group has both a radial and an axial
1729 component. This geometry is not supported with constraint
1732 .. mdp-value:: angle
1734 Pull along an angle defined by four groups. The angle is
1735 defined as the angle between two vectors: the vector connecting
1736 the COM of the first group to the COM of the second group and
1737 the vector connecting the COM of the third group to the COM of
1740 .. mdp-value:: angle-axis
1742 As :mdp-value:`angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1743 Thus, only the two groups that define the first vector need to be given.
1745 .. mdp-value:: dihedral
1747 Pull along a dihedral angle defined by six groups. These pairwise
1748 define three vectors: the vector connecting the COM of group 1
1749 to the COM of group 2, the COM of group 3 to the COM of group 4,
1750 and the COM of group 5 to the COM group 6. The dihedral angle is
1751 then defined as the angle between two planes: the plane spanned by the
1752 the two first vectors and the plane spanned the two last vectors.
1755 .. mdp:: pull-coord1-groups
1757 The group indices on which this pull coordinate will operate.
1758 The number of group indices required is geometry dependent.
1759 The first index can be 0, in which case an
1760 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1761 absolute reference the system is no longer translation invariant
1762 and one should think about what to do with the center of mass
1765 .. mdp:: pull-coord1-dim
1768 Selects the dimensions that this pull coordinate acts on and that
1769 are printed to the output files when
1770 :mdp:`pull-print-components` = :mdp-value:`yes`. With
1771 :mdp:`pull-coord1-geometry` = :mdp-value:`distance`, only Cartesian
1772 components set to Y contribute to the distance. Thus setting this
1773 to Y Y N results in a distance in the x/y plane. With other
1774 geometries all dimensions with non-zero entries in
1775 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1776 dimensions only affect the output.
1778 .. mdp:: pull-coord1-origin
1781 The pull reference position for use with an absolute reference.
1783 .. mdp:: pull-coord1-vec
1786 The pull direction. :ref:`gmx grompp` normalizes the vector.
1788 .. mdp:: pull-coord1-start
1792 do not modify :mdp:`pull-coord1-init`
1796 add the COM distance of the starting conformation to
1797 :mdp:`pull-coord1-init`
1799 .. mdp:: pull-coord1-init
1801 (0.0) \[nm\] / \[deg\]
1802 The reference distance at t=0.
1804 .. mdp:: pull-coord1-rate
1806 (0) \[nm/ps\] / \[deg/ps\]
1807 The rate of change of the reference position.
1809 .. mdp:: pull-coord1-k
1811 (0) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\]
1812 The force constant. For umbrella pulling this is the harmonic force
1813 constant in kJ mol-1 nm-2 (or kJ mol-1 rad-2 for angles). For constant force pulling this is the
1814 force constant of the linear potential, and thus the negative (!)
1815 of the constant force in kJ mol-1 nm-1 (or kJ mol-1 rad-1 for angles).
1816 Note that for angles the force constant is expressed in terms of radians
1817 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1819 .. mdp:: pull-coord1-kB
1821 (pull-k1) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\]
1822 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1823 :mdp:`free-energy` is turned on. The force constant is then (1 -
1824 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1830 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
1831 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
1832 that can be used to achieve such a rotation.
1838 No enforced rotation will be applied. All enforced rotation options will
1839 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1844 Apply the rotation potential specified by :mdp:`rot-type` to the group of atoms given
1845 under the :mdp:`rot-group` option.
1847 .. mdp:: rot-ngroups
1850 Number of rotation groups.
1854 Name of rotation group 0 in the index file.
1859 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
1860 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
1861 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
1866 Use mass weighted rotation group positions.
1871 Rotation vector, will get normalized.
1876 Pivot point (nm) for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
1881 Reference rotation rate (degree/ps) of group 0.
1886 Force constant (kJ/(mol*nm^2)) for group 0.
1888 .. mdp:: rot-slab-dist0
1891 Slab distance (nm), if a flexible axis rotation type was chosen.
1893 .. mdp:: rot-min-gauss0
1896 Minimum value (cutoff) of Gaussian function for the force to be evaluated
1897 (for the flexible axis potentials).
1902 Value of additive constant epsilon' (nm^2) for ``rm2*`` and ``flex2*`` potentials.
1904 .. mdp:: rot-fit-method0
1907 Fitting method when determining the actual angle of a rotation group
1908 (can be one of ``rmsd``, ``norm``, or ``potential``).
1910 .. mdp:: rot-potfit-nsteps0
1913 For fit type ``potential``, the number of angular positions around the reference angle for which the
1914 rotation potential is evaluated.
1916 .. mdp:: rot-potfit-step0
1919 For fit type ``potential``, the distance in degrees between two angular positions.
1921 .. mdp:: rot-nstrout
1924 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
1925 and the rotation potential energy.
1927 .. mdp:: rot-nstsout
1930 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
1940 ignore distance restraint information in topology file
1942 .. mdp-value:: simple
1944 simple (per-molecule) distance restraints.
1946 .. mdp-value:: ensemble
1948 distance restraints over an ensemble of molecules in one
1949 simulation box. Normally, one would perform ensemble averaging
1950 over multiple subsystems, each in a separate box, using ``mdrun
1951 -multi``. Supply ``topol0.tpr``, ``topol1.tpr``, ... with
1952 different coordinates and/or velocities. The environment
1953 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
1954 within each ensemble (usually equal to the ``mdrun -multi``
1957 .. mdp:: disre-weighting
1959 .. mdp-value:: equal
1961 divide the restraint force equally over all atom pairs in the
1964 .. mdp-value:: conservative
1966 the forces are the derivative of the restraint potential, this
1967 results in an weighting of the atom pairs to the reciprocal
1968 seventh power of the displacement. The forces are conservative
1969 when :mdp:`disre-tau` is zero.
1971 .. mdp:: disre-mixed
1975 the violation used in the calculation of the restraint force is
1976 the time-averaged violation
1980 the violation used in the calculation of the restraint force is
1981 the square root of the product of the time-averaged violation
1982 and the instantaneous violation
1986 (1000) \[kJ mol-1 nm-2\]
1987 force constant for distance restraints, which is multiplied by a
1988 (possibly) different factor for each restraint given in the `fac`
1989 column of the interaction in the topology file.
1994 time constant for distance restraints running average. A value of
1995 zero turns off time averaging.
1997 .. mdp:: nstdisreout
2000 period between steps when the running time-averaged and
2001 instantaneous distances of all atom pairs involved in restraints
2002 are written to the energy file (can make the energy file very
2009 ignore orientation restraint information in topology file
2013 use orientation restraints, ensemble averaging can be performed
2019 force constant for orientation restraints, which is multiplied by a
2020 (possibly) different weight factor for each restraint, can be set
2021 to zero to obtain the orientations from a free simulation
2026 time constant for orientation restraints running average. A value
2027 of zero turns off time averaging.
2029 .. mdp:: orire-fitgrp
2031 fit group for orientation restraining. This group of atoms is used
2032 to determine the rotation **R** of the system with respect to the
2033 reference orientation. The reference orientation is the starting
2034 conformation of the first subsystem. For a protein, backbone is a
2037 .. mdp:: nstorireout
2040 period between steps when the running time-averaged and
2041 instantaneous orientations for all restraints, and the molecular
2042 order tensor are written to the energy file (can make the energy
2046 Free energy calculations
2047 ^^^^^^^^^^^^^^^^^^^^^^^^
2049 .. mdp:: free-energy
2053 Only use topology A.
2057 Interpolate between topology A (lambda=0) to topology B
2058 (lambda=1) and write the derivative of the Hamiltonian with
2059 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2060 or the Hamiltonian differences with respect to other lambda
2061 values (as specified with foreign lambda) to the energy file
2062 and/or to ``dhdl.xvg``, where they can be processed by, for
2063 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2064 are interpolated linearly as described in the manual. When
2065 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2066 used for the LJ and Coulomb interactions.
2070 Turns on expanded ensemble simulation, where the alchemical state
2071 becomes a dynamic variable, allowing jumping between different
2072 Hamiltonians. See the expanded ensemble options for controlling how
2073 expanded ensemble simulations are performed. The different
2074 Hamiltonians used in expanded ensemble simulations are defined by
2075 the other free energy options.
2077 .. mdp:: init-lambda
2080 starting value for lambda (float). Generally, this should only be
2081 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2082 other cases, :mdp:`init-lambda-state` should be specified
2083 instead. Must be greater than or equal to 0.
2085 .. mdp:: delta-lambda
2088 increment per time step for lambda
2090 .. mdp:: init-lambda-state
2093 starting value for the lambda state (integer). Specifies which
2094 columm of the lambda vector (:mdp:`coul-lambdas`,
2095 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2096 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2097 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2098 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2099 the first column, and so on.
2101 .. mdp:: fep-lambdas
2104 Zero, one or more lambda values for which Delta H values will be
2105 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2106 steps. Values must be between 0 and 1. Free energy differences
2107 between different lambda values can then be determined with
2108 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2109 other -lambdas keywords because all components of the lambda vector
2110 that are not specified will use :mdp:`fep-lambdas` (including
2111 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2113 .. mdp:: coul-lambdas
2116 Zero, one or more lambda values for which Delta H values will be
2117 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2118 steps. Values must be between 0 and 1. Only the electrostatic
2119 interactions are controlled with this component of the lambda
2120 vector (and only if the lambda=0 and lambda=1 states have differing
2121 electrostatic interactions).
2123 .. mdp:: vdw-lambdas
2126 Zero, one or more lambda values for which Delta H values will be
2127 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2128 steps. Values must be between 0 and 1. Only the van der Waals
2129 interactions are controlled with this component of the lambda
2132 .. mdp:: bonded-lambdas
2135 Zero, one or more lambda values for which Delta H values will be
2136 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2137 steps. Values must be between 0 and 1. Only the bonded interactions
2138 are controlled with this component of the lambda vector.
2140 .. mdp:: restraint-lambdas
2143 Zero, one or more lambda values for which Delta H values will be
2144 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2145 steps. Values must be between 0 and 1. Only the restraint
2146 interactions: dihedral restraints, and the pull code restraints are
2147 controlled with this component of the lambda vector.
2149 .. mdp:: mass-lambdas
2152 Zero, one or more lambda values for which Delta H values will be
2153 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2154 steps. Values must be between 0 and 1. Only the particle masses are
2155 controlled with this component of the lambda vector.
2157 .. mdp:: temperature-lambdas
2160 Zero, one or more lambda values for which Delta H values will be
2161 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2162 steps. Values must be between 0 and 1. Only the temperatures
2163 controlled with this component of the lambda vector. Note that
2164 these lambdas should not be used for replica exchange, only for
2165 simulated tempering.
2167 .. mdp:: calc-lambda-neighbors
2170 Controls the number of lambda values for which Delta H values will
2171 be calculated and written out, if :mdp:`init-lambda-state` has
2172 been set. A positive value will limit the number of lambda points
2173 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2174 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2175 has a value of 2, energies for lambda points 3-7 will be calculated
2176 and writen out. A value of -1 means all lambda points will be
2177 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2178 1 is sufficient, while for MBAR -1 should be used.
2183 the soft-core alpha parameter, a value of 0 results in linear
2184 interpolation of the LJ and Coulomb interactions
2189 the power of the radial term in the soft-core equation. Possible
2190 values are 6 and 48. 6 is more standard, and is the default. When
2191 48 is used, then sc-alpha should generally be much lower (between
2197 Whether to apply the soft-core free energy interaction
2198 transformation to the Columbic interaction of a molecule. Default
2199 is no, as it is generally more efficient to turn off the Coulomic
2200 interactions linearly before turning off the van der Waals
2201 interactions. Note that it is only taken into account when lambda
2202 states are used, not with :mdp:`couple-lambda0` /
2203 :mdp:`couple-lambda1`, and you can still turn off soft-core
2204 interactions by setting :mdp:`sc-alpha` to 0.
2209 the power for lambda in the soft-core function, only the values 1
2215 the soft-core sigma for particles which have a C6 or C12 parameter
2216 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2218 .. mdp:: couple-moltype
2220 Here one can supply a molecule type (as defined in the topology)
2221 for calculating solvation or coupling free energies. There is a
2222 special option ``system`` that couples all molecule types in the
2223 system. This can be useful for equilibrating a system starting from
2224 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2225 on. The Van der Waals interactions and/or charges in this molecule
2226 type can be turned on or off between lambda=0 and lambda=1,
2227 depending on the settings of :mdp:`couple-lambda0` and
2228 :mdp:`couple-lambda1`. If you want to decouple one of several
2229 copies of a molecule, you need to copy and rename the molecule
2230 definition in the topology.
2232 .. mdp:: couple-lambda0
2234 .. mdp-value:: vdw-q
2236 all interactions are on at lambda=0
2240 the charges are zero (no Coulomb interactions) at lambda=0
2244 the Van der Waals interactions are turned at lambda=0; soft-core
2245 interactions will be required to avoid singularities
2249 the Van der Waals interactions are turned off and the charges
2250 are zero at lambda=0; soft-core interactions will be required to
2251 avoid singularities.
2253 .. mdp:: couple-lambda1
2255 analogous to :mdp:`couple-lambda1`, but for lambda=1
2257 .. mdp:: couple-intramol
2261 All intra-molecular non-bonded interactions for moleculetype
2262 :mdp:`couple-moltype` are replaced by exclusions and explicit
2263 pair interactions. In this manner the decoupled state of the
2264 molecule corresponds to the proper vacuum state without
2265 periodicity effects.
2269 The intra-molecular Van der Waals and Coulomb interactions are
2270 also turned on/off. This can be useful for partitioning
2271 free-energies of relatively large molecules, where the
2272 intra-molecular non-bonded interactions might lead to
2273 kinetically trapped vacuum conformations. The 1-4 pair
2274 interactions are not turned off.
2279 the frequency for writing dH/dlambda and possibly Delta H to
2280 dhdl.xvg, 0 means no ouput, should be a multiple of
2281 :mdp:`nstcalcenergy`.
2283 .. mdp:: dhdl-derivatives
2287 If yes (the default), the derivatives of the Hamiltonian with
2288 respect to lambda at each :mdp:`nstdhdl` step are written
2289 out. These values are needed for interpolation of linear energy
2290 differences with :ref:`gmx bar` (although the same can also be
2291 achieved with the right foreign lambda setting, that may not be as
2292 flexible), or with thermodynamic integration
2294 .. mdp:: dhdl-print-energy
2298 Include either the total or the potential energy in the dhdl
2299 file. Options are 'no', 'potential', or 'total'. This information
2300 is needed for later free energy analysis if the states of interest
2301 are at different temperatures. If all states are at the same
2302 temperature, this information is not needed. 'potential' is useful
2303 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2304 file. When rerunning from an existing trajectory, the kinetic
2305 energy will often not be correct, and thus one must compute the
2306 residual free energy from the potential alone, with the kinetic
2307 energy component computed analytically.
2309 .. mdp:: separate-dhdl-file
2313 The free energy values that are calculated (as specified with
2314 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2315 written out to a separate file, with the default name
2316 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2321 The free energy values are written out to the energy output file
2322 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2323 steps), where they can be extracted with :ref:`gmx energy` or
2324 used directly with :ref:`gmx bar`.
2326 .. mdp:: dh-hist-size
2329 If nonzero, specifies the size of the histogram into which the
2330 Delta H values (specified with foreign lambda) and the derivative
2331 dH/dl values are binned, and written to ener.edr. This can be used
2332 to save disk space while calculating free energy differences. One
2333 histogram gets written for each foreign lambda and two for the
2334 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2335 histogram settings (too small size or too wide bins) can introduce
2336 errors. Do not use histograms unless you're certain you need it.
2338 .. mdp:: dh-hist-spacing
2341 Specifies the bin width of the histograms, in energy units. Used in
2342 conjunction with :mdp:`dh-hist-size`. This size limits the
2343 accuracy with which free energies can be calculated. Do not use
2344 histograms unless you're certain you need it.
2347 Expanded Ensemble calculations
2348 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2350 .. mdp:: nstexpanded
2352 The number of integration steps beween attempted moves changing the
2353 system Hamiltonian in expanded ensemble simulations. Must be a
2354 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2361 No Monte Carlo in state space is performed.
2363 .. mdp-value:: metropolis-transition
2365 Uses the Metropolis weights to update the expanded ensemble
2366 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2369 .. mdp-value:: barker-transition
2371 Uses the Barker transition critera to update the expanded
2372 ensemble weight of each state i, defined by exp(-beta_new
2373 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2375 .. mdp-value:: wang-landau
2377 Uses the Wang-Landau algorithm (in state space, not energy
2378 space) to update the expanded ensemble weights.
2380 .. mdp-value:: min-variance
2382 Uses the minimum variance updating method of Escobedo et al. to
2383 update the expanded ensemble weights. Weights will not be the
2384 free energies, but will rather emphasize states that need more
2385 sampling to give even uncertainty.
2387 .. mdp:: lmc-mc-move
2391 No Monte Carlo in state space is performed.
2393 .. mdp-value:: metropolis-transition
2395 Randomly chooses a new state up or down, then uses the
2396 Metropolis critera to decide whether to accept or reject:
2397 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2399 .. mdp-value:: barker-transition
2401 Randomly chooses a new state up or down, then uses the Barker
2402 transition critera to decide whether to accept or reject:
2403 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2405 .. mdp-value:: gibbs
2407 Uses the conditional weights of the state given the coordinate
2408 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2411 .. mdp-value:: metropolized-gibbs
2413 Uses the conditional weights of the state given the coordinate
2414 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2415 to move to, EXCLUDING the current state, then uses a rejection
2416 step to ensure detailed balance. Always more efficient that
2417 Gibbs, though only marginally so in many situations, such as
2418 when only the nearest neighbors have decent phase space
2424 random seed to use for Monte Carlo moves in state space. When
2425 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2427 .. mdp:: mc-temperature
2429 Temperature used for acceptance/rejection for Monte Carlo moves. If
2430 not specified, the temperature of the simulation specified in the
2431 first group of :mdp:`ref-t` is used.
2436 The cutoff for the histogram of state occupancies to be reset, and
2437 the free energy incrementor to be changed from delta to delta *
2438 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2439 each histogram) / (average number of samples at each
2440 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2441 histogram is only considered flat if all Nratio > 0.8 AND
2442 simultaneously all 1/Nratio > 0.8.
2447 Each time the histogram is considered flat, then the current value
2448 of the Wang-Landau incrementor for the free energies is multiplied
2449 by :mdp:`wl-scale`. Value must be between 0 and 1.
2451 .. mdp:: init-wl-delta
2454 The initial value of the Wang-Landau incrementor in kT. Some value
2455 near 1 kT is usually most efficient, though sometimes a value of
2456 2-3 in units of kT works better if the free energy differences are
2459 .. mdp:: wl-oneovert
2462 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2463 the large sample limit. There is significant evidence that the
2464 standard Wang-Landau algorithms in state space presented here
2465 result in free energies getting 'burned in' to incorrect values
2466 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2467 then when the incrementor becomes less than 1/N, where N is the
2468 mumber of samples collected (and thus proportional to the data
2469 collection time, hence '1 over t'), then the Wang-Lambda
2470 incrementor is set to 1/N, decreasing every step. Once this occurs,
2471 :mdp:`wl-ratio` is ignored, but the weights will still stop
2472 updating when the equilibration criteria set in
2473 :mdp:`lmc-weights-equil` is achieved.
2475 .. mdp:: lmc-repeats
2478 Controls the number of times that each Monte Carlo swap type is
2479 performed each iteration. In the limit of large numbers of Monte
2480 Carlo repeats, then all methods converge to Gibbs sampling. The
2481 value will generally not need to be different from 1.
2483 .. mdp:: lmc-gibbsdelta
2486 Limit Gibbs sampling to selected numbers of neighboring states. For
2487 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2488 sampling over all of the states that are defined. A positive value
2489 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2490 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2491 value of -1 means that all states are considered. For less than 100
2492 states, it is probably not that expensive to include all states.
2494 .. mdp:: lmc-forced-nstart
2497 Force initial state space sampling to generate weights. In order to
2498 come up with reasonable initial weights, this setting allows the
2499 simulation to drive from the initial to the final lambda state,
2500 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2501 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2502 sufficiently long (thousands of steps, perhaps), then the weights
2503 will be close to correct. However, in most cases, it is probably
2504 better to simply run the standard weight equilibration algorithms.
2506 .. mdp:: nst-transition-matrix
2509 Frequency of outputting the expanded ensemble transition matrix. A
2510 negative number means it will only be printed at the end of the
2513 .. mdp:: symmetrized-transition-matrix
2516 Whether to symmetrize the empirical transition matrix. In the
2517 infinite limit the matrix will be symmetric, but will diverge with
2518 statistical noise for short timescales. Forced symmetrization, by
2519 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2520 like the existence of (small magnitude) negative eigenvalues.
2522 .. mdp:: mininum-var-min
2525 The min-variance strategy (option of :mdp:`lmc-stats` is only
2526 valid for larger number of samples, and can get stuck if too few
2527 samples are used at each state. :mdp:`mininum-var-min` is the
2528 minimum number of samples that each state that are allowed before
2529 the min-variance strategy is activated if selected.
2531 .. mdp:: init-lambda-weights
2533 The initial weights (free energies) used for the expanded ensemble
2534 states. Default is a vector of zero weights. format is similar to
2535 the lambda vector settings in :mdp:`fep-lambdas`, except the
2536 weights can be any floating point number. Units are kT. Its length
2537 must match the lambda vector lengths.
2539 .. mdp:: lmc-weights-equil
2543 Expanded ensemble weights continue to be updated throughout the
2548 The input expanded ensemble weights are treated as equilibrated,
2549 and are not updated throughout the simulation.
2551 .. mdp-value:: wl-delta
2553 Expanded ensemble weight updating is stopped when the
2554 Wang-Landau incrementor falls below this value.
2556 .. mdp-value:: number-all-lambda
2558 Expanded ensemble weight updating is stopped when the number of
2559 samples at all of the lambda states is greater than this value.
2561 .. mdp-value:: number-steps
2563 Expanded ensemble weight updating is stopped when the number of
2564 steps is greater than the level specified by this value.
2566 .. mdp-value:: number-samples
2568 Expanded ensemble weight updating is stopped when the number of
2569 total samples across all lambda states is greater than the level
2570 specified by this value.
2572 .. mdp-value:: count-ratio
2574 Expanded ensemble weight updating is stopped when the ratio of
2575 samples at the least sampled lambda state and most sampled
2576 lambda state greater than this value.
2578 .. mdp:: simulated-tempering
2581 Turn simulated tempering on or off. Simulated tempering is
2582 implemented as expanded ensemble sampling with different
2583 temperatures instead of different Hamiltonians.
2585 .. mdp:: sim-temp-low
2588 Low temperature for simulated tempering.
2590 .. mdp:: sim-temp-high
2593 High temperature for simulated tempering.
2595 .. mdp:: simulated-tempering-scaling
2597 Controls the way that the temperatures at intermediate lambdas are
2598 calculated from the :mdp:`temperature-lambdas` part of the lambda
2601 .. mdp-value:: linear
2603 Linearly interpolates the temperatures using the values of
2604 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2605 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2606 a temperature of 350. A nonlinear set of temperatures can always
2607 be implemented with uneven spacing in lambda.
2609 .. mdp-value:: geometric
2611 Interpolates temperatures geometrically between
2612 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2613 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2614 :mdp:`sim-temp-low`) raised to the power of
2615 (i/(ntemps-1)). This should give roughly equal exchange for
2616 constant heat capacity, though of course things simulations that
2617 involve protein folding have very high heat capacity peaks.
2619 .. mdp-value:: exponential
2621 Interpolates temperatures exponentially between
2622 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2623 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2624 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2625 (i))-1)/(exp(1.0)-i)).
2633 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2634 in groups Protein and Sol will experience constant acceleration as
2635 specified in the :mdp:`accelerate` line
2640 acceleration for :mdp:`acc-grps`; x, y and z for each group
2641 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2642 constant acceleration of 0.1 nm ps-2 in X direction, second group
2647 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2648 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2649 specifies for which dimension the freezing applies. To avoid
2650 spurious contibrutions to the virial and pressure due to large
2651 forces between completely frozen atoms you need to use energy group
2652 exclusions, this also saves computing time. Note that coordinates
2653 of frozen atoms are not scaled by pressure-coupling algorithms.
2657 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2658 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
2659 N N N N`` means that particles in the first group can move only in
2660 Z direction. The particles in the second group can move in any
2663 .. mdp:: cos-acceleration
2666 the amplitude of the acceleration profile for calculating the
2667 viscosity. The acceleration is in the X-direction and the magnitude
2668 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2669 added to the energy file: the amplitude of the velocity profile and
2674 (0 0 0 0 0 0) \[nm ps-1\]
2675 The velocities of deformation for the box elements: a(x) b(y) c(z)
2676 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2677 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2678 elements are corrected for periodicity. The coordinates are
2679 transformed accordingly. Frozen degrees of freedom are (purposely)
2680 also transformed. The time ts is set to t at the first step and at
2681 steps at which x and v are written to trajectory to ensure exact
2682 restarts. Deformation can be used together with semiisotropic or
2683 anisotropic pressure coupling when the appropriate
2684 compressibilities are set to zero. The diagonal elements can be
2685 used to strain a solid. The off-diagonal elements can be used to
2686 shear a solid or a liquid.
2692 .. mdp:: E-x ; E-y ; E-z
2694 If you want to use an electric field in a direction, enter 3
2695 numbers after the appropriate E-direction, the first number: the
2696 number of cosines, only 1 is implemented (with frequency 0) so
2697 enter 1, the second number: the strength of the electric field in V
2698 nm^-1, the third number: the phase of the cosine, you can enter any
2699 number here since a cosine of frequency zero has no phase.
2701 .. mdp:: E-xt; E-yt; E-zt
2703 Here you can specify a pulsed alternating electric field. The field
2704 has the form of a gaussian laser pulse:
2706 E(t) = E0 exp ( -(t-t0)^2/(2 sigma^2) ) cos(omega (t-t0))
2708 For example, the four parameters for direction x are set in the
2709 three fields of :mdp:`E-x` and :mdp:`E-xt` like
2713 E-xt = omega t0 sigma
2715 In the special case that sigma = 0, the exponential term is omitted
2716 and only the cosine term is used.
2718 More details in Carl Caleman and David van der Spoel: Picosecond
2719 Melting of Ice by an Infrared Laser Pulse - A Simulation Study
2720 Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008)
2724 Mixed quantum/classical molecular dynamics
2725 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2735 Do a QM/MM simulation. Several groups can be described at
2736 different QM levels separately. These are specified in the
2737 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
2738 initio* theory at which the groups are described is specified by
2739 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
2740 groups at different levels of theory is only possible with the
2741 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
2745 groups to be descibed at the QM level
2749 .. mdp-value:: normal
2751 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
2752 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
2753 *ab initio* theory. The rest of the system is described at the
2754 MM level. The QM and MM subsystems interact as follows: MM point
2755 charges are included in the QM one-electron hamiltonian and all
2756 Lennard-Jones interactions are described at the MM level.
2758 .. mdp-value:: ONIOM
2760 The interaction between the subsystem is described using the
2761 ONIOM method by Morokuma and co-workers. There can be more than
2762 one :mdp:`QMMM-grps` each modeled at a different level of QM
2763 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
2768 Method used to compute the energy and gradients on the QM
2769 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
2770 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
2771 included in the active space is specified by :mdp:`CASelectrons`
2772 and :mdp:`CASorbitals`.
2777 Basis set used to expand the electronic wavefuntion. Only Gaussian
2778 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
2779 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
2784 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
2785 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
2786 layer needs to be specified separately.
2791 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
2792 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
2793 needs to be specified separately.
2795 .. mdp:: CASorbitals
2798 The number of orbitals to be included in the active space when
2799 doing a CASSCF computation.
2801 .. mdp:: CASelectrons
2804 The number of electrons to be included in the active space when
2805 doing a CASSCF computation.
2811 No surface hopping. The system is always in the electronic
2816 Do a QM/MM MD simulation on the excited state-potential energy
2817 surface and enforce a *diabatic* hop to the ground-state when
2818 the system hits the conical intersection hyperline in the course
2819 the simulation. This option only works in combination with the
2826 .. mdp:: implicit-solvent
2834 Do a simulation with implicit solvent using the Generalized Born
2835 formalism. Three different methods for calculating the Born
2836 radii are available, Still, HCT and OBC. These are specified
2837 with the :mdp:`gb-algorithm` field. The non-polar solvation is
2838 specified with the :mdp:`sa-algorithm` field.
2840 .. mdp:: gb-algorithm
2842 .. mdp-value:: Still
2844 Use the Still method to calculate the Born radii
2848 Use the Hawkins-Cramer-Truhlar method to calculate the Born
2853 Use the Onufriev-Bashford-Case method to calculate the Born
2859 Frequency to (re)-calculate the Born radii. For most practial
2860 purposes, setting a value larger than 1 violates energy
2861 conservation and leads to unstable trajectories.
2866 Cut-off for the calculation of the Born radii. Currently must be
2869 .. mdp:: gb-epsilon-solvent
2872 Dielectric constant for the implicit solvent
2874 .. mdp:: gb-saltconc
2877 Salt concentration for implicit solvent models, currently not used
2879 .. mdp:: gb-obc-alpha
2880 .. mdp:: gb-obc-beta
2881 .. mdp:: gb-obc-gamma
2883 Scale factors for the OBC model. Default values of 1, 0.78 and 4.85
2884 respectively are for OBC(II). Values for OBC(I) are 0.8, 0 and 2.91
2887 .. mdp:: gb-dielectric-offset
2890 Distance for the di-electric offset when calculating the Born
2891 radii. This is the offset between the center of each atom the
2892 center of the polarization energy for the corresponding atom
2894 .. mdp:: sa-algorithm
2896 .. mdp-value:: Ace-approximation
2898 Use an Ace-type approximation
2902 No non-polar solvation calculation done. For GBSA only the polar
2903 part gets calculated
2905 .. mdp:: sa-surface-tension
2908 Default value for surface tension with SA algorithms. The default
2909 value is -1; Note that if this default value is not changed it will
2910 be overridden by :ref:`gmx grompp` using values that are specific
2911 for the choice of radii algorithm (0.0049 kcal/mol/Angstrom^2 for
2912 Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will
2913 while using an sa-algorithm other than None means no non-polar
2914 calculations are done.
2917 Computational Electrophysiology
2918 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2919 Use these options to switch on and control ion/water position exchanges in "Computational
2920 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
2926 Do not enable ion/water position exchanges.
2928 .. mdp-value:: X ; Y ; Z
2930 Allow for ion/water position exchanges along the chosen direction.
2931 In a typical setup with the membranes parallel to the x-y plane,
2932 ion/water pairs need to be exchanged in Z direction to sustain the
2933 requested ion concentrations in the compartments.
2935 .. mdp:: swap-frequency
2937 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
2938 per compartment are determined and exchanges made if necessary.
2939 Normally it is not necessary to check at every time step.
2940 For typical Computational Electrophysiology setups, a value of about 100 is
2941 sufficient and yields a negligible performance impact.
2943 .. mdp:: split-group0
2945 Name of the index group of the membrane-embedded part of channel #0.
2946 The center of mass of these atoms defines one of the compartment boundaries
2947 and should be chosen such that it is near the center of the membrane.
2949 .. mdp:: split-group1
2951 Channel #1 defines the position of the other compartment boundary.
2953 .. mdp:: massw-split0
2955 (no) Defines whether or not mass-weighting is used to calculate the split group center.
2959 Use the geometrical center.
2963 Use the center of mass.
2965 .. mdp:: massw-split1
2967 (no) As above, but for split-group #1.
2969 .. mdp:: solvent-group
2971 Name of the index group of solvent molecules.
2973 .. mdp:: coupl-steps
2975 (\10) Average the number of ions per compartment over these many swap attempt steps.
2976 This can be used to prevent that ions near a compartment boundary
2977 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
2981 (1) The number of different ion types to be controlled. These are during the
2982 simulation exchanged with solvent molecules to reach the desired reference numbers.
2984 .. mdp:: iontype0-name
2986 Name of the first ion type.
2988 .. mdp:: iontype0-in-A
2990 (-1) Requested (=reference) number of ions of type 0 in compartment A.
2991 The default value of -1 means: use the number of ions as found in time step 0
2994 .. mdp:: iontype0-in-B
2996 (-1) Reference number of ions of type 0 for compartment B.
2998 .. mdp:: bulk-offsetA
3000 (0.0) Offset of the first swap layer from the compartment A midplane.
3001 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3002 at maximum distance (= bulk concentration) to the split group layers. However,
3003 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3004 towards one of the compartment-partitioning layers (at +/- 1.0).
3006 .. mdp:: bulk-offsetB
3008 (0.0) Offset of the other swap layer from the compartment B midplane.
3013 (\1) Only swap ions if threshold difference to requested count is reached.
3017 (2.0) \[nm\] Radius of the split cylinder #0.
3018 Two split cylinders (mimicking the channel pores) can optionally be defined
3019 relative to the center of the split group. With the help of these cylinders
3020 it can be counted which ions have passed which channel. The split cylinder
3021 definition has no impact on whether or not ion/water swaps are done.
3025 (1.0) \[nm\] Upper extension of the split cylinder #0.
3029 (1.0) \[nm\] Lower extension of the split cylinder #0.
3033 (2.0) \[nm\] Radius of the split cylinder #1.
3037 (1.0) \[nm\] Upper extension of the split cylinder #1.
3041 (1.0) \[nm\] Lower extension of the split cylinder #1.
3044 User defined thingies
3045 ^^^^^^^^^^^^^^^^^^^^^
3049 .. mdp:: userint1 (0)
3050 .. mdp:: userint2 (0)
3051 .. mdp:: userint3 (0)
3052 .. mdp:: userint4 (0)
3053 .. mdp:: userreal1 (0)
3054 .. mdp:: userreal2 (0)
3055 .. mdp:: userreal3 (0)
3056 .. mdp:: userreal4 (0)
3058 These you can use if you modify code. You can pass integers and
3059 reals and groups to your subroutine. Check the inputrec definition
3060 in ``src/gromacs/mdtypes/inputrec.h``
3065 This feature has been removed from |Gromacs|, but so that old
3066 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3067 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3068 fatal error if this is set.
3074 .. _reference manual: gmx-manual-parent-dir_
biod.pnpi.spb.ru / alexxy / gromacs.git / blob