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.
214 .. mdp-value:: Linear
216 Remove center of mass translation
218 .. mdp-value:: Angular
220 Remove center of mass translation and rotation around the center of mass
224 No restriction on the center of mass motion
229 frequency for center of mass motion removal
233 group(s) for center of mass motion removal, default is the whole
243 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
244 the friction coefficient for each particle is calculated as mass/
250 used to initialize random generator for thermal noise for
251 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
252 a pseudo random seed is used. When running BD or SD on multiple
253 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
254 the processor number.
262 (10.0) \[kJ mol-1 nm-1\]
263 the minimization is converged when the maximum force is smaller
274 frequency of performing 1 steepest descent step while doing
275 conjugate gradient energy minimization.
280 Number of correction steps to use for L-BFGS minimization. A higher
281 number is (at least theoretically) more accurate, but slower.
284 Shell Molecular Dynamics
285 ^^^^^^^^^^^^^^^^^^^^^^^^
287 When shells or flexible constraints are present in the system the
288 positions of the shells and the lengths of the flexible constraints
289 are optimized at every time step until either the RMS force on the
290 shells and constraints is less than :mdp:`emtol`, or a maximum number
291 of iterations :mdp:`niter` has been reached. Minimization is converged
292 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
293 value should be 1.0 at most.
298 maximum number of iterations for optimizing the shell positions and
299 the flexible constraints.
304 the step size for optimizing the flexible constraints. Should be
305 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
306 particles in a flexible constraint and d2V/dq2 is the second
307 derivative of the potential in the constraint direction. Hopefully
308 this number does not differ too much between the flexible
309 constraints, as the number of iterations and thus the runtime is
310 very sensitive to fcstep. Try several values!
313 Test particle insertion
314 ^^^^^^^^^^^^^^^^^^^^^^^
319 the test particle insertion radius, see integrators
320 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
329 number of steps that elapse between writing coordinates to output
330 trajectory file, the last coordinates are always written
335 number of steps that elapse between writing velocities to output
336 trajectory, the last velocities are always written
341 number of steps that elapse between writing forces to output
347 number of steps that elapse between writing energies to the log
348 file, the last energies are always written
350 .. mdp:: nstcalcenergy
353 number of steps that elapse between calculating the energies, 0 is
354 never. This option is only relevant with dynamics. This option affects the
355 performance in parallel simulations, because calculating energies
356 requires global communication between all processes which can
357 become a bottleneck at high parallelization.
362 number of steps that else between writing energies to energy file,
363 the last energies are always written, should be a multiple of
364 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
365 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
366 energy file, so :ref:`gmx energy` can report exact energy averages
367 and fluctuations also when :mdp:`nstenergy` > 1
369 .. mdp:: nstxout-compressed
372 number of steps that elapse between writing position coordinates
373 using lossy compression
375 .. mdp:: compressed-x-precision
378 precision with which to write to the compressed trajectory file
380 .. mdp:: compressed-x-grps
382 group(s) to write to the compressed trajectory file, by default the
383 whole system is written (if :mdp:`nstxout-compressed` > 0)
387 group(s) for which to write to write short-ranged non-bonded
388 potential energies to the energy file (not supported on GPUs)
394 .. mdp:: cutoff-scheme
396 .. mdp-value:: Verlet
398 Generate a pair list with buffering. The buffer size is
399 automatically set based on :mdp:`verlet-buffer-tolerance`,
400 unless this is set to -1, in which case :mdp:`rlist` will be
401 used. This option has an explicit, exact cut-off at :mdp:`rvdw`
402 equal to :mdp:`rcoulomb`, unless PME or Ewald is used, in which
403 case :mdp:`rcoulomb` > :mdp:`rvdw` is allowed. Currently only
404 cut-off, reaction-field, PME or Ewald electrostatics and plain
405 LJ are supported. Some :ref:`gmx mdrun` functionality is not yet
406 supported with the :mdp:`Verlet` scheme, but :ref:`gmx grompp`
407 checks for this. Native GPU acceleration is only supported with
408 :mdp:`Verlet`. With GPU-accelerated PME or with separate PME
409 ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
410 balance by scaling :mdp:`rcoulomb` and the grid spacing. This
411 can be turned off with ``mdrun -notunepme``. :mdp:`Verlet` is
412 faster than :mdp:`group` when there is no water, or if
413 :mdp:`group` would use a pair-list buffer to conserve energy.
417 Generate a pair list for groups of atoms. These groups
418 correspond to the charge groups in the topology. This was the
419 only cut-off treatment scheme before version 4.6, and is
420 **deprecated in |gmx-version|**. There is no explicit buffering of
421 the pair list. This enables efficient force calculations for
422 water, but energy is only conserved when a buffer is explicitly
431 Frequency to update the neighbor list. When this is 0, the
432 neighbor list is made only once. With energy minimization the
433 neighborlist will be updated for every energy evaluation when
434 :mdp:`nstlist` is greater than 0. With :mdp:`Verlet` and
435 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
436 a minimum value and :ref:`gmx mdrun` might increase it, unless
437 it is set to 1. With parallel simulations and/or non-bonded
438 force calculation on the GPU, a value of 20 or 40 often gives
439 the best performance. With :mdp:`group` and non-exact
440 cut-off's, :mdp:`nstlist` will affect the accuracy of your
441 simulation and it can not be chosen freely.
445 The neighbor list is only constructed once and never
446 updated. This is mainly useful for vacuum simulations in which
447 all particles see each other.
457 Make a grid in the box and only check atoms in neighboring grid
458 cells when constructing a new neighbor list every
459 :mdp:`nstlist` steps. In large systems grid search is much
460 faster than simple search.
462 .. mdp-value:: simple
464 Check every atom in the box when constructing a new neighbor
465 list every :mdp:`nstlist` steps (only with :mdp:`group`
472 Use periodic boundary conditions in all directions.
476 Use no periodic boundary conditions, ignore the box. To simulate
477 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
478 best performance without cut-offs on a single MPI rank, set
479 :mdp:`nstlist` to zero and :mdp:`ns-type` =simple.
483 Use periodic boundary conditions in x and y directions
484 only. This works only with :mdp:`ns-type` =grid and can be used
485 in combination with walls_. Without walls or with only one wall
486 the system size is infinite in the z direction. Therefore
487 pressure coupling or Ewald summation methods can not be
488 used. These disadvantages do not apply when two walls are used.
490 .. mdp:: periodic-molecules
494 molecules are finite, fast molecular PBC can be used
498 for systems with molecules that couple to themselves through the
499 periodic boundary conditions, this requires a slower PBC
500 algorithm and molecules are not made whole in the output
502 .. mdp:: verlet-buffer-tolerance
504 (0.005) \[kJ/mol/ps\]
506 Useful only with the :mdp:`Verlet` :mdp:`cutoff-scheme`. This sets
507 the maximum allowed error for pair interactions per particle caused
508 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
509 :mdp:`nstlist` and the Verlet buffer size are fixed (for
510 performance reasons), particle pairs not in the pair list can
511 occasionally get within the cut-off distance during
512 :mdp:`nstlist` -1 steps. This causes very small jumps in the
513 energy. In a constant-temperature ensemble, these very small energy
514 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
515 estimate assumes a homogeneous particle distribution, hence the
516 errors might be slightly underestimated for multi-phase
517 systems. (See the `reference manual`_ for details). For longer
518 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
519 overestimated, because the interactions between particles are
520 ignored. Combined with cancellation of errors, the actual drift of
521 the total energy is usually one to two orders of magnitude
522 smaller. Note that the generated buffer size takes into account
523 that the |Gromacs| pair-list setup leads to a reduction in the
524 drift by a factor 10, compared to a simple particle-pair based
525 list. Without dynamics (energy minimization etc.), the buffer is 5%
526 of the cut-off. For NVE simulations the initial temperature is
527 used, unless this is zero, in which case a buffer of 10% is
528 used. For NVE simulations the tolerance usually needs to be lowered
529 to achieve proper energy conservation on the nanosecond time
530 scale. To override the automated buffer setting, use
531 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
536 Cut-off distance for the short-range neighbor list. With the
537 :mdp:`Verlet` :mdp:`cutoff-scheme`, this is by default set by the
538 :mdp:`verlet-buffer-tolerance` option and the value of
539 :mdp:`rlist` is ignored.
547 .. mdp-value:: Cut-off
549 Plain cut-off with neighborlist radius :mdp:`rlist` and
550 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
555 Classical Ewald sum electrostatics. The real-space cut-off
556 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
557 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
558 of wave vectors used in reciprocal space is controlled by
559 :mdp:`fourierspacing`. The relative accuracy of
560 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
562 NOTE: Ewald scales as O(N^3/2) and is thus extremely slow for
563 large systems. It is included mainly for reference - in most
564 cases PME will perform much better.
568 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
569 space is similar to the Ewald sum, while the reciprocal part is
570 performed with FFTs. Grid dimensions are controlled with
571 :mdp:`fourierspacing` and the interpolation order with
572 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
573 interpolation the electrostatic forces have an accuracy of
574 2-3*10^-4. Since the error from the vdw-cutoff is larger than
575 this you might try 0.15 nm. When running in parallel the
576 interpolation parallelizes better than the FFT, so try
577 decreasing grid dimensions while increasing interpolation.
579 .. mdp-value:: P3M-AD
581 Particle-Particle Particle-Mesh algorithm with analytical
582 derivative for for long range electrostatic interactions. The
583 method and code is identical to SPME, except that the influence
584 function is optimized for the grid. This gives a slight increase
587 .. mdp-value:: Reaction-Field
589 Reaction field electrostatics with Coulomb cut-off
590 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
591 dielectric constant beyond the cut-off is
592 :mdp:`epsilon-rf`. The dielectric constant can be set to
593 infinity by setting :mdp:`epsilon-rf` =0.
595 .. mdp-value:: Generalized-Reaction-Field
597 Generalized reaction field with Coulomb cut-off
598 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rcoulomb`. The
599 dielectric constant beyond the cut-off is
600 :mdp:`epsilon-rf`. The ionic strength is computed from the
601 number of charged (*i.e.* with non zero charge) charge
602 groups. The temperature for the GRF potential is set with
605 .. mdp-value:: Reaction-Field-zero
607 In |Gromacs|, normal reaction-field electrostatics with
608 :mdp:`cutoff-scheme` = :mdp:`group` leads to bad energy
609 conservation. :mdp:`Reaction-Field-zero` solves this by making
610 the potential zero beyond the cut-off. It can only be used with
611 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
612 only for that value the force vanishes at the
613 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
614 :mdp:`rcoulomb` to accommodate for the size of charge groups
615 and diffusion between neighbor list updates. This, and the fact
616 that table lookups are used instead of analytical functions make
617 :mdp:`Reaction-Field-zero` computationally more expensive than
618 normal reaction-field.
622 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
623 might want to use :mdp:`Reaction-Field-zero` instead, which has
624 a similar potential shape, but has a physical interpretation and
625 has better energies due to the exclusion correction terms.
627 .. mdp-value:: Encad-Shift
629 The Coulomb potential is decreased over the whole range, using
630 the definition from the Encad simulation package.
632 .. mdp-value:: Switch
634 Analogous to :mdp-value:`vdwtype=Switch` for
635 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
636 serious artifacts, advice: use :mdp:`Reaction-Field-zero`
641 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
642 with user-defined potential functions for repulsion, dispersion
643 and Coulomb. When pair interactions are present, :ref:`gmx
644 mdrun` also expects to find a file ``tablep.xvg`` for the pair
645 interactions. When the same interactions should be used for
646 non-bonded and pair interactions the user can specify the same
647 file name for both table files. These files should contain 7
648 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
649 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
650 function, ``g(x)`` the dispersion function and ``h(x)`` the
651 repulsion function. When :mdp:`vdwtype` is not set to User the
652 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
653 the non-bonded interactions ``x`` values should run from 0 to
654 the largest cut-off distance + :mdp:`table-extension` and
655 should be uniformly spaced. For the pair interactions the table
656 length in the file will be used. The optimal spacing, which is
657 used for non-user tables, is ``0.002 nm`` when you run in mixed
658 precision or ``0.0005 nm`` when you run in double precision. The
659 function value at ``x=0`` is not important. More information is
660 in the printed manual.
662 .. mdp-value:: PME-Switch
664 A combination of PME and a switch function for the direct-space
665 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
666 :mdp:`rlist`. This is mainly useful constant energy simulations
667 (note that using PME with :mdp:`cutoff-scheme` = :mdp:`Verlet`
668 will be more efficient).
670 .. mdp-value:: PME-User
672 A combination of PME and user tables (see
673 above). :mdp:`rcoulomb` is allowed to be smaller than
674 :mdp:`rlist`. The PME mesh contribution is subtracted from the
675 user table by :ref:`gmx mdrun`. Because of this subtraction the
676 user tables should contain about 10 decimal places.
678 .. mdp-value:: PME-User-Switch
680 A combination of PME-User and a switching function (see
681 above). The switching function is applied to final
682 particle-particle interaction, *i.e.* both to the user supplied
683 function and the PME Mesh correction part.
685 .. mdp:: coulomb-modifier
687 .. mdp-value:: Potential-shift-Verlet
689 Selects Potential-shift with the Verlet cutoff-scheme, as it is
690 (nearly) free; selects None with the group cutoff-scheme.
692 .. mdp-value:: Potential-shift
694 Shift the Coulomb potential by a constant such that it is zero
695 at the cut-off. This makes the potential the integral of the
696 force. Note that this does not affect the forces or the
701 Use an unmodified Coulomb potential. With the group scheme this
702 means no exact cut-off is used, energies and forces are
703 calculated for all pairs in the neighborlist.
705 .. mdp:: rcoulomb-switch
708 where to start switching the Coulomb potential, only relevant
709 when force or potential switching is used
714 distance for the Coulomb cut-off
719 The relative dielectric constant. A value of 0 means infinity.
724 The relative dielectric constant of the reaction field. This
725 is only used with reaction-field electrostatics. A value of 0
734 .. mdp-value:: Cut-off
736 Twin range cut-offs with neighbor list cut-off :mdp:`rlist` and
737 VdW cut-off :mdp:`rvdw`, where :mdp:`rvdw` >= :mdp:`rlist`.
741 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
742 grid dimensions are controlled with :mdp:`fourierspacing` in
743 the same way as for electrostatics, and the interpolation order
744 is controlled with :mdp:`pme-order`. The relative accuracy of
745 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
746 and the specific combination rules that are to be used by the
747 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
751 This functionality is deprecated and replaced by
752 :mdp:`vdw-modifier` = Force-switch. The LJ (not Buckingham)
753 potential is decreased over the whole range and the forces decay
754 smoothly to zero between :mdp:`rvdw-switch` and
755 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
756 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
757 size of charge groups and diffusion between neighbor list
760 .. mdp-value:: Switch
762 This functionality is deprecated and replaced by
763 :mdp:`vdw-modifier` = Potential-switch. The LJ (not Buckingham)
764 potential is normal out to :mdp:`rvdw-switch`, after which it
765 is switched off to reach zero at :mdp:`rvdw`. Both the
766 potential and force functions are continuously smooth, but be
767 aware that all switch functions will give rise to a bulge
768 (increase) in the force (since we are switching the
769 potential). The neighbor search cut-off :mdp:`rlist` should be
770 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
771 size of charge groups and diffusion between neighbor list
774 .. mdp-value:: Encad-Shift
776 The LJ (not Buckingham) potential is decreased over the whole
777 range, using the definition from the Encad simulation package.
781 See user for :mdp:`coulombtype`. The function value at zero is
782 not important. When you want to use LJ correction, make sure
783 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
784 function. When :mdp:`coulombtype` is not set to User the values
785 for the ``f`` and ``-f'`` columns are ignored.
787 .. mdp:: vdw-modifier
789 .. mdp-value:: Potential-shift-Verlet
791 Selects Potential-shift with the Verlet cutoff-scheme, as it is
792 (nearly) free; selects None with the group cutoff-scheme.
794 .. mdp-value:: Potential-shift
796 Shift the Van der Waals potential by a constant such that it is
797 zero at the cut-off. This makes the potential the integral of
798 the force. Note that this does not affect the forces or the
803 Use an unmodified Van der Waals potential. With the group scheme
804 this means no exact cut-off is used, energies and forces are
805 calculated for all pairs in the neighborlist.
807 .. mdp-value:: Force-switch
809 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
810 and :mdp:`rvdw`. This shifts the potential shift over the whole
811 range and switches it to zero at the cut-off. Note that this is
812 more expensive to calculate than a plain cut-off and it is not
813 required for energy conservation, since Potential-shift
814 conserves energy just as well.
816 .. mdp-value:: Potential-switch
818 Smoothly switches the potential to zero between
819 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
820 articifically large forces in the switching region and is much
821 more expensive to calculate. This option should only be used if
822 the force field you are using requires this.
828 where to start switching the LJ force and possibly the potential,
829 only relevant when force or potential switching is used
834 distance for the LJ or Buckingham cut-off
840 don't apply any correction
842 .. mdp-value:: EnerPres
844 apply long range dispersion corrections for Energy and Pressure
848 apply long range dispersion corrections for Energy only
854 .. mdp:: table-extension
857 Extension of the non-bonded potential lookup tables beyond the
858 largest cut-off distance. The value should be large enough to
859 account for charge group sizes and the diffusion between
860 neighbor-list updates. Without user defined potential the same
861 table length is used for the lookup tables for the 1-4
862 interactions, which are always tabulated irrespective of the use of
863 tables for the non-bonded interactions. The value of
864 :mdp:`table-extension` in no way affects the values of
865 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
867 .. mdp:: energygrp-table
869 When user tables are used for electrostatics and/or VdW, here one
870 can give pairs of energy groups for which seperate user tables
871 should be used. The two energy groups will be appended to the table
872 file name, in order of their definition in :mdp:`energygrps`,
873 seperated by underscores. For example, if ``energygrps = Na Cl
874 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
875 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
876 normal ``table.xvg`` which will be used for all other energy group
883 .. mdp:: fourierspacing
886 For ordinary Ewald, the ratio of the box dimensions and the spacing
887 determines a lower bound for the number of wave vectors to use in
888 each (signed) direction. For PME and P3M, that ratio determines a
889 lower bound for the number of Fourier-space grid points that will
890 be used along that axis. In all cases, the number for each
891 direction can be overridden by entering a non-zero value for that
892 :mdp:`fourier-nx` direction. For optimizing the relative load of
893 the particle-particle interactions and the mesh part of PME, it is
894 useful to know that the accuracy of the electrostatics remains
895 nearly constant when the Coulomb cut-off and the PME grid spacing
896 are scaled by the same factor.
903 Highest magnitude of wave vectors in reciprocal space when using Ewald.
904 Grid size when using PME or P3M. These values override
905 :mdp:`fourierspacing` per direction. The best choice is powers of
906 2, 3, 5 and 7. Avoid large primes.
911 Interpolation order for PME. 4 equals cubic interpolation. You
912 might try 6/8/10 when running in parallel and simultaneously
913 decrease grid dimension.
918 The relative strength of the Ewald-shifted direct potential at
919 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
920 will give a more accurate direct sum, but then you need more wave
921 vectors for the reciprocal sum.
923 .. mdp:: ewald-rtol-lj
926 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
927 to control the relative strength of the dispersion potential at
928 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
929 electrostatic potential.
931 .. mdp:: lj-pme-comb-rule
934 The combination rules used to combine VdW-parameters in the
935 reciprocal part of LJ-PME. Geometric rules are much faster than
936 Lorentz-Berthelot and usually the recommended choice, even when the
937 rest of the force field uses the Lorentz-Berthelot rules.
939 .. mdp-value:: Geometric
941 Apply geometric combination rules
943 .. mdp-value:: Lorentz-Berthelot
945 Apply Lorentz-Berthelot combination rules
947 .. mdp:: ewald-geometry
951 The Ewald sum is performed in all three dimensions.
955 The reciprocal sum is still performed in 3D, but a force and
956 potential correction applied in the `z` dimension to produce a
957 pseudo-2D summation. If your system has a slab geometry in the
958 `x-y` plane you can try to increase the `z`-dimension of the box
959 (a box height of 3 times the slab height is usually ok) and use
962 .. mdp:: epsilon-surface
965 This controls the dipole correction to the Ewald summation in
966 3D. The default value of zero means it is turned off. Turn it on by
967 setting it to the value of the relative permittivity of the
968 imaginary surface around your infinite system. Be careful - you
969 shouldn't use this if you have free mobile charges in your
970 system. This value does not affect the slab 3DC variant of the long
981 No temperature coupling.
983 .. mdp-value:: berendsen
985 Temperature coupling with a Berendsen-thermostat to a bath with
986 temperature :mdp:`ref-t`, with time constant
987 :mdp:`tau-t`. Several groups can be coupled separately, these
988 are specified in the :mdp:`tc-grps` field separated by spaces.
990 .. mdp-value:: nose-hoover
992 Temperature coupling using a Nose-Hoover extended ensemble. The
993 reference temperature and coupling groups are selected as above,
994 but in this case :mdp:`tau-t` controls the period of the
995 temperature fluctuations at equilibrium, which is slightly
996 different from a relaxation time. For NVT simulations the
997 conserved energy quantity is written to energy and log file.
999 .. mdp-value:: andersen
1001 Temperature coupling by randomizing a fraction of the particles
1002 at each timestep. Reference temperature and coupling groups are
1003 selected as above. :mdp:`tau-t` is the average time between
1004 randomization of each molecule. Inhibits particle dynamics
1005 somewhat, but little or no ergodicity issues. Currently only
1006 implemented with velocity Verlet, and not implemented with
1009 .. mdp-value:: andersen-massive
1011 Temperature coupling by randomizing all particles at infrequent
1012 timesteps. Reference temperature and coupling groups are
1013 selected as above. :mdp:`tau-t` is the time between
1014 randomization of all molecules. Inhibits particle dynamics
1015 somewhat, but little or no ergodicity issues. Currently only
1016 implemented with velocity Verlet.
1018 .. mdp-value:: v-rescale
1020 Temperature coupling using velocity rescaling with a stochastic
1021 term (JCP 126, 014101). This thermostat is similar to Berendsen
1022 coupling, with the same scaling using :mdp:`tau-t`, but the
1023 stochastic term ensures that a proper canonical ensemble is
1024 generated. The random seed is set with :mdp:`ld-seed`. This
1025 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1026 simulations the conserved energy quantity is written to the
1027 energy and log file.
1032 The frequency for coupling the temperature. The default value of -1
1033 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1034 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1035 Verlet integrators :mdp:`nsttcouple` is set to 1.
1037 .. mdp:: nh-chain-length
1040 The number of chained Nose-Hoover thermostats for velocity Verlet
1041 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1042 only supports 1. Data for the NH chain variables is not printed to
1043 the :ref:`edr` file, but can be using the ``GMX_NOSEHOOVER_CHAINS``
1044 environment variable
1048 groups to couple to separate temperature baths
1053 time constant for coupling (one for each group in
1054 :mdp:`tc-grps`), -1 means no temperature coupling
1059 reference temperature for coupling (one for each group in
1070 No pressure coupling. This means a fixed box size.
1072 .. mdp-value:: Berendsen
1074 Exponential relaxation pressure coupling with time constant
1075 :mdp:`tau-p`. The box is scaled every timestep. It has been
1076 argued that this does not yield a correct thermodynamic
1077 ensemble, but it is the most efficient way to scale a box at the
1080 .. mdp-value:: Parrinello-Rahman
1082 Extended-ensemble pressure coupling where the box vectors are
1083 subject to an equation of motion. The equation of motion for the
1084 atoms is coupled to this. No instantaneous scaling takes
1085 place. As for Nose-Hoover temperature coupling the time constant
1086 :mdp:`tau-p` is the period of pressure fluctuations at
1087 equilibrium. This is probably a better method when you want to
1088 apply pressure scaling during data collection, but beware that
1089 you can get very large oscillations if you are starting from a
1090 different pressure. For simulations where the exact fluctation
1091 of the NPT ensemble are important, or if the pressure coupling
1092 time is very short it may not be appropriate, as the previous
1093 time step pressure is used in some steps of the |Gromacs|
1094 implementation for the current time step pressure.
1098 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1099 :mdp-value:`md-vv` or :mdp-value:`md-vv-avek`, very similar to
1100 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1101 time constant :mdp:`tau-p` is the period of pressure
1102 fluctuations at equilibrium. This is probably a better method
1103 when you want to apply pressure scaling during data collection,
1104 but beware that you can get very large oscillations if you are
1105 starting from a different pressure. Currently (as of version
1106 5.1), it only supports isotropic scaling, and only works without
1111 .. mdp-value:: isotropic
1113 Isotropic pressure coupling with time constant
1114 :mdp:`tau-p`. The compressibility and reference pressure are
1115 set with :mdp:`compressibility` and :mdp:`ref-p`, one value is
1118 .. mdp-value:: semiisotropic
1120 Pressure coupling which is isotropic in the ``x`` and ``y``
1121 direction, but different in the ``z`` direction. This can be
1122 useful for membrane simulations. 2 values are needed for ``x/y``
1123 and ``z`` directions respectively.
1125 .. mdp-value:: anisotropic
1127 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1128 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1129 respectively. When the off-diagonal compressibilities are set to
1130 zero, a rectangular box will stay rectangular. Beware that
1131 anisotropic scaling can lead to extreme deformation of the
1134 .. mdp-value:: surface-tension
1136 Surface tension coupling for surfaces parallel to the
1137 xy-plane. Uses normal pressure coupling for the `z`-direction,
1138 while the surface tension is coupled to the `x/y` dimensions of
1139 the box. The first :mdp:`ref-p` value is the reference surface
1140 tension times the number of surfaces ``bar nm``, the second
1141 value is the reference `z`-pressure ``bar``. The two
1142 :mdp:`compressibility` values are the compressibility in the
1143 `x/y` and `z` direction respectively. The value for the
1144 `z`-compressibility should be reasonably accurate since it
1145 influences the convergence of the surface-tension, it can also
1146 be set to zero to have a box with constant height.
1151 The frequency for coupling the pressure. The default value of -1
1152 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1153 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1154 Verlet integrators :mdp:`nstpcouple` is set to 1.
1159 time constant for coupling
1161 .. mdp:: compressibility
1164 compressibility (NOTE: this is now really in bar-1) For water at 1
1165 atm and 300 K the compressibility is 4.5e-5 bar^-1.
1170 reference pressure for coupling
1172 .. mdp:: refcoord-scaling
1176 The reference coordinates for position restraints are not
1177 modified. Note that with this option the virial and pressure
1178 will depend on the absolute positions of the reference
1183 The reference coordinates are scaled with the scaling matrix of
1184 the pressure coupling.
1188 Scale the center of mass of the reference coordinates with the
1189 scaling matrix of the pressure coupling. The vectors of each
1190 reference coordinate to the center of mass are not scaled. Only
1191 one COM is used, even when there are multiple molecules with
1192 position restraints. For calculating the COM of the reference
1193 coordinates in the starting configuration, periodic boundary
1194 conditions are not taken into account.
1200 Simulated annealing is controlled separately for each temperature
1201 group in |Gromacs|. The reference temperature is a piecewise linear
1202 function, but you can use an arbitrary number of points for each
1203 group, and choose either a single sequence or a periodic behaviour for
1204 each group. The actual annealing is performed by dynamically changing
1205 the reference temperature used in the thermostat algorithm selected,
1206 so remember that the system will usually not instantaneously reach the
1207 reference temperature!
1211 Type of annealing for each temperature group
1215 No simulated annealing - just couple to reference temperature value.
1217 .. mdp-value:: single
1219 A single sequence of annealing points. If your simulation is
1220 longer than the time of the last point, the temperature will be
1221 coupled to this constant value after the annealing sequence has
1222 reached the last time point.
1224 .. mdp-value:: periodic
1226 The annealing will start over at the first reference point once
1227 the last reference time is reached. This is repeated until the
1230 .. mdp:: annealing-npoints
1232 A list with the number of annealing reference/control points used
1233 for each temperature group. Use 0 for groups that are not
1234 annealed. The number of entries should equal the number of
1237 .. mdp:: annealing-time
1239 List of times at the annealing reference/control points for each
1240 group. If you are using periodic annealing, the times will be used
1241 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1242 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1243 etc. The number of entries should equal the sum of the numbers
1244 given in :mdp:`annealing-npoints`.
1246 .. mdp:: annealing-temp
1248 List of temperatures at the annealing reference/control points for
1249 each group. The number of entries should equal the sum of the
1250 numbers given in :mdp:`annealing-npoints`.
1252 Confused? OK, let's use an example. Assume you have two temperature
1253 groups, set the group selections to ``annealing = single periodic``,
1254 the number of points of each group to ``annealing-npoints = 3 4``, the
1255 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1256 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1257 will be coupled to 298K at 0ps, but the reference temperature will
1258 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1259 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1260 second group is coupled to 298K at 0ps, it increases linearly to 320K
1261 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1262 decreases to 298K, and then it starts over with the same pattern
1263 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1264 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1274 Do not generate velocities. The velocities are set to zero
1275 when there are no velocities in the input structure file.
1279 Generate velocities in :ref:`gmx grompp` according to a
1280 Maxwell distribution at temperature :mdp:`gen-temp`, with
1281 random seed :mdp:`gen-seed`. This is only meaningful with
1282 integrator :mdp-value:`integrator=md`.
1287 temperature for Maxwell distribution
1292 used to initialize random generator for random velocities,
1293 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1300 .. mdp:: constraints
1304 No constraints except for those defined explicitly in the
1305 topology, *i.e.* bonds are represented by a harmonic (or other)
1306 potential or a Morse potential (depending on the setting of
1307 :mdp:`morse`) and angles by a harmonic (or other) potential.
1309 .. mdp-value:: h-bonds
1311 Convert the bonds with H-atoms to constraints.
1313 .. mdp-value:: all-bonds
1315 Convert all bonds to constraints.
1317 .. mdp-value:: h-angles
1319 Convert all bonds and additionally the angles that involve
1320 H-atoms to bond-constraints.
1322 .. mdp-value:: all-angles
1324 Convert all bonds and angles to bond-constraints.
1326 .. mdp:: constraint-algorithm
1328 .. mdp-value:: LINCS
1330 LINear Constraint Solver. With domain decomposition the parallel
1331 version P-LINCS is used. The accuracy in set with
1332 :mdp:`lincs-order`, which sets the number of matrices in the
1333 expansion for the matrix inversion. After the matrix inversion
1334 correction the algorithm does an iterative correction to
1335 compensate for lengthening due to rotation. The number of such
1336 iterations can be controlled with :mdp:`lincs-iter`. The root
1337 mean square relative constraint deviation is printed to the log
1338 file every :mdp:`nstlog` steps. If a bond rotates more than
1339 :mdp:`lincs-warnangle` in one step, a warning will be printed
1340 both to the log file and to ``stderr``. LINCS should not be used
1341 with coupled angle constraints.
1343 .. mdp-value:: SHAKE
1345 SHAKE is slightly slower and less stable than LINCS, but does
1346 work with angle constraints. The relative tolerance is set with
1347 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1348 does not support constraints between atoms on different nodes,
1349 thus it can not be used with domain decompositon when inter
1350 charge-group constraints are present. SHAKE can not be used with
1351 energy minimization.
1353 .. mdp:: continuation
1355 This option was formerly known as unconstrained-start.
1359 apply constraints to the start configuration and reset shells
1363 do not apply constraints to the start configuration and do not
1364 reset shells, useful for exact coninuation and reruns
1369 relative tolerance for SHAKE
1371 .. mdp:: lincs-order
1374 Highest order in the expansion of the constraint coupling
1375 matrix. When constraints form triangles, an additional expansion of
1376 the same order is applied on top of the normal expansion only for
1377 the couplings within such triangles. For "normal" MD simulations an
1378 order of 4 usually suffices, 6 is needed for large time-steps with
1379 virtual sites or BD. For accurate energy minimization an order of 8
1380 or more might be required. With domain decomposition, the cell size
1381 is limited by the distance spanned by :mdp:`lincs-order` +1
1382 constraints. When one wants to scale further than this limit, one
1383 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1384 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1385 )* :mdp:`lincs-order` remains constant.
1390 Number of iterations to correct for rotational lengthening in
1391 LINCS. For normal runs a single step is sufficient, but for NVE
1392 runs where you want to conserve energy accurately or for accurate
1393 energy minimization you might want to increase it to 2.
1395 .. mdp:: lincs-warnangle
1398 maximum angle that a bond can rotate before LINCS will complain
1404 bonds are represented by a harmonic potential
1408 bonds are represented by a Morse potential
1411 Energy group exclusions
1412 ^^^^^^^^^^^^^^^^^^^^^^^
1414 .. mdp:: energygrp-excl
1416 Pairs of energy groups for which all non-bonded interactions are
1417 excluded. An example: if you have two energy groups ``Protein`` and
1418 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1419 would give only the non-bonded interactions between the protein and
1420 the solvent. This is especially useful for speeding up energy
1421 calculations with ``mdrun -rerun`` and for excluding interactions
1422 within frozen groups.
1431 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1432 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1433 ``=xy``. When set to 2 pressure coupling and Ewald summation can be
1434 used (it is usually best to use semiisotropic pressure coupling
1435 with the ``x/y`` compressibility set to 0, as otherwise the surface
1436 area will change). Walls interact wit the rest of the system
1437 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1438 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1439 monitor the interaction of energy groups with each wall. The center
1440 of mass motion removal will be turned off in the ``z``-direction.
1442 .. mdp:: wall-atomtype
1444 the atom type name in the force field for each wall. By (for
1445 example) defining a special wall atom type in the topology with its
1446 own combination rules, this allows for independent tuning of the
1447 interaction of each atomtype with the walls.
1453 LJ integrated over the volume behind the wall: 9-3 potential
1457 LJ integrated over the wall surface: 10-4 potential
1461 direct LJ potential with the ``z`` distance from the wall
1465 user defined potentials indexed with the ``z`` distance from the
1466 wall, the tables are read analogously to the
1467 :mdp:`energygrp-table` option, where the first name is for a
1468 "normal" energy group and the second name is ``wall0`` or
1469 ``wall1``, only the dispersion and repulsion columns are used
1471 .. mdp:: wall-r-linpot
1474 Below this distance from the wall the potential is continued
1475 linearly and thus the force is constant. Setting this option to a
1476 postive value is especially useful for equilibration when some
1477 atoms are beyond a wall. When the value is <=0 (<0 for
1478 :mdp:`wall-type` =table), a fatal error is generated when atoms
1481 .. mdp:: wall-density
1484 the number density of the atoms for each wall for wall types 9-3
1487 .. mdp:: wall-ewald-zfac
1490 The scaling factor for the third box vector for Ewald summation
1491 only, the minimum is 2. Ewald summation can only be used with
1492 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1493 ``=3dc``. The empty layer in the box serves to decrease the
1494 unphysical Coulomb interaction between periodic images.
1500 Note that where pulling coordinate are applicable, there can be more
1501 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1502 variables will exist accordingly. Documentation references to things
1503 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1504 applicable pulling coordinate.
1510 No center of mass pulling. All the following pull options will
1511 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1516 Center of mass pulling will be applied on 1 or more groups using
1517 1 or more pull coordinates.
1519 .. mdp:: pull-cylinder-r
1522 the radius of the cylinder for
1523 :mdp:`pull-coord1-geometry` = :mdp-value:`cylinder`
1525 .. mdp:: pull-constr-tol
1528 the relative constraint tolerance for constraint pulling
1530 .. mdp:: pull-print-com
1534 do not print the COM for any group
1538 print the COM of all groups for all pull coordinates
1540 .. mdp:: pull-print-ref-value
1544 do not print the reference value for each pull coordinate
1548 print the reference value for each pull coordinate
1550 .. mdp:: pull-print-components
1554 only print the distance for each pull coordinate
1558 print the distance and Cartesian components selected in
1559 :mdp:`pull-coord1-dim`
1561 .. mdp:: pull-nstxout
1564 frequency for writing out the COMs of all the pull group (0 is
1567 .. mdp:: pull-nstfout
1570 frequency for writing out the force of all the pulled group
1574 .. mdp:: pull-ngroups
1577 The number of pull groups, not including the absolute reference
1578 group, when used. Pull groups can be reused in multiple pull
1579 coordinates. Below only the pull options for group 1 are given,
1580 further groups simply increase the group index number.
1582 .. mdp:: pull-ncoords
1585 The number of pull coordinates. Below only the pull options for
1586 coordinate 1 are given, further coordinates simply increase the
1587 coordinate index number.
1589 .. mdp:: pull-group1-name
1591 The name of the pull group, is looked up in the index file or in
1592 the default groups to obtain the atoms involved.
1594 .. mdp:: pull-group1-weights
1596 Optional relative weights which are multiplied with the masses of
1597 the atoms to give the total weight for the COM. The number should
1598 be 0, meaning all 1, or the number of atoms in the pull group.
1600 .. mdp:: pull-group1-pbcatom
1603 The reference atom for the treatment of periodic boundary
1604 conditions inside the group (this has no effect on the treatment of
1605 the pbc between groups). This option is only important when the
1606 diameter of the pull group is larger than half the shortest box
1607 vector. For determining the COM, all atoms in the group are put at
1608 their periodic image which is closest to
1609 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1610 atom (number wise) is used. This parameter is not used with
1611 :mdp:`pull-group1-geometry` cylinder. A value of -1 turns on cosine
1612 weighting, which is useful for a group of molecules in a periodic
1613 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1616 .. mdp:: pull-coord1-type
1618 .. mdp-value:: umbrella
1620 Center of mass pulling using an umbrella potential between the
1621 reference group and one or more groups.
1623 .. mdp-value:: constraint
1625 Center of mass pulling using a constraint between the reference
1626 group and one or more groups. The setup is identical to the
1627 option umbrella, except for the fact that a rigid constraint is
1628 applied instead of a harmonic potential.
1630 .. mdp-value:: constant-force
1632 Center of mass pulling using a linear potential and therefore a
1633 constant force. For this option there is no reference position
1634 and therefore the parameters :mdp:`pull-coord1-init` and
1635 :mdp:`pull-coord1-rate` are not used.
1637 .. mdp-value:: flat-bottom
1639 At distances above :mdp:`pull-coord1-init` a harmonic potential
1640 is applied, otherwise no potential is applied.
1642 .. mdp-value:: flat-bottom-high
1644 At distances below :mdp:`pull-coord1-init` a harmonic potential
1645 is applied, otherwise no potential is applied.
1647 .. mdp-value:: external-potential
1649 An external potential that needs to be provided by another
1652 .. mdp:: pull-coord1-potential-provider
1654 The name of the external module that provides the potential for
1655 the case where :mdp:`pull-coord1-type` is external-potential.
1657 .. mdp:: pull-coord1-geometry
1659 .. mdp-value:: distance
1661 Pull along the vector connecting the two groups. Components can
1662 be selected with :mdp:`pull-coord1-dim`.
1664 .. mdp-value:: direction
1666 Pull in the direction of :mdp:`pull-coord1-vec`.
1668 .. mdp-value:: direction-periodic
1670 As :mdp-value:`direction`, but allows the distance to be larger
1671 than half the box size. With this geometry the box should not be
1672 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1673 the pull force is not added to virial.
1675 .. mdp-value:: direction-relative
1677 As :mdp-value:`direction`, but the pull vector is the vector
1678 that points from the COM of a third to the COM of a fourth pull
1679 group. This means that 4 groups need to be supplied in
1680 :mdp:`pull-coord1-groups`. Note that the pull force will give
1681 rise to a torque on the pull vector, which is turn leads to
1682 forces perpendicular to the pull vector on the two groups
1683 defining the vector. If you want a pull group to move between
1684 the two groups defining the vector, simply use the union of
1685 these two groups as the reference group.
1687 .. mdp-value:: cylinder
1689 Designed for pulling with respect to a layer where the reference
1690 COM is given by a local cylindrical part of the reference group.
1691 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1692 the first of the two groups in :mdp:`pull-coord1-groups` a
1693 cylinder is selected around the axis going through the COM of
1694 the second group with direction :mdp:`pull-coord1-vec` with
1695 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1696 continously to zero as the radial distance goes from 0 to
1697 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1698 dependence gives rise to radial forces on both pull groups.
1699 Note that the radius should be smaller than half the box size.
1700 For tilted cylinders they should be even smaller than half the
1701 box size since the distance of an atom in the reference group
1702 from the COM of the pull group has both a radial and an axial
1703 component. This geometry is not supported with constraint
1706 .. mdp-value:: angle
1708 Pull along an angle defined by four groups. The angle is
1709 defined as the angle between two vectors: the vector connecting
1710 the COM of the first group to the COM of the second group and
1711 the vector connecting the COM of the third group to the COM of
1714 .. mdp-value:: angle-axis
1716 As :mdp-value:`angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1717 Thus, only the two groups that define the first vector need to be given.
1719 .. mdp-value:: dihedral
1721 Pull along a dihedral angle defined by six groups. These pairwise
1722 define three vectors: the vector connecting the COM of group 1
1723 to the COM of group 2, the COM of group 3 to the COM of group 4,
1724 and the COM of group 5 to the COM group 6. The dihedral angle is
1725 then defined as the angle between two planes: the plane spanned by the
1726 the two first vectors and the plane spanned the two last vectors.
1729 .. mdp:: pull-coord1-groups
1731 The group indices on which this pull coordinate will operate.
1732 The number of group indices required is geometry dependent.
1733 The first index can be 0, in which case an
1734 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1735 absolute reference the system is no longer translation invariant
1736 and one should think about what to do with the center of mass
1739 .. mdp:: pull-coord1-dim
1742 Selects the dimensions that this pull coordinate acts on and that
1743 are printed to the output files when
1744 :mdp:`pull-print-components` = :mdp-value:`yes`. With
1745 :mdp:`pull-coord1-geometry` = :mdp-value:`distance`, only Cartesian
1746 components set to Y contribute to the distance. Thus setting this
1747 to Y Y N results in a distance in the x/y plane. With other
1748 geometries all dimensions with non-zero entries in
1749 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1750 dimensions only affect the output.
1752 .. mdp:: pull-coord1-origin
1755 The pull reference position for use with an absolute reference.
1757 .. mdp:: pull-coord1-vec
1760 The pull direction. :ref:`gmx grompp` normalizes the vector.
1762 .. mdp:: pull-coord1-start
1766 do not modify :mdp:`pull-coord1-init`
1770 add the COM distance of the starting conformation to
1771 :mdp:`pull-coord1-init`
1773 .. mdp:: pull-coord1-init
1775 (0.0) \[nm\] / \[deg\]
1776 The reference distance at t=0.
1778 .. mdp:: pull-coord1-rate
1780 (0) \[nm/ps\] / \[deg/ps\]
1781 The rate of change of the reference position.
1783 .. mdp:: pull-coord1-k
1785 (0) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\]
1786 The force constant. For umbrella pulling this is the harmonic force
1787 constant in kJ mol-1 nm-2 (or kJ mol-1 rad-2 for angles). For constant force pulling this is the
1788 force constant of the linear potential, and thus the negative (!)
1789 of the constant force in kJ mol-1 nm-1 (or kJ mol-1 rad-1 for angles).
1790 Note that for angles the force constant is expressed in terms of radians
1791 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1793 .. mdp:: pull-coord1-kB
1795 (pull-k1) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\] / \[kJ mol-1 rad-2\] / \[kJ mol-1 rad-1\]
1796 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1797 :mdp:`free-energy` is turned on. The force constant is then (1 -
1798 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1808 ignore distance restraint information in topology file
1810 .. mdp-value:: simple
1812 simple (per-molecule) distance restraints.
1814 .. mdp-value:: ensemble
1816 distance restraints over an ensemble of molecules in one
1817 simulation box. Normally, one would perform ensemble averaging
1818 over multiple subsystems, each in a separate box, using ``mdrun
1819 -multi``. Supply ``topol0.tpr``, ``topol1.tpr``, ... with
1820 different coordinates and/or velocities. The environment
1821 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
1822 within each ensemble (usually equal to the ``mdrun -multi``
1825 .. mdp:: disre-weighting
1827 .. mdp-value:: equal
1829 divide the restraint force equally over all atom pairs in the
1832 .. mdp-value:: conservative
1834 the forces are the derivative of the restraint potential, this
1835 results in an weighting of the atom pairs to the reciprocal
1836 seventh power of the displacement. The forces are conservative
1837 when :mdp:`disre-tau` is zero.
1839 .. mdp:: disre-mixed
1843 the violation used in the calculation of the restraint force is
1844 the time-averaged violation
1848 the violation used in the calculation of the restraint force is
1849 the square root of the product of the time-averaged violation
1850 and the instantaneous violation
1854 (1000) \[kJ mol-1 nm-2\]
1855 force constant for distance restraints, which is multiplied by a
1856 (possibly) different factor for each restraint given in the `fac`
1857 column of the interaction in the topology file.
1862 time constant for distance restraints running average. A value of
1863 zero turns off time averaging.
1865 .. mdp:: nstdisreout
1868 period between steps when the running time-averaged and
1869 instantaneous distances of all atom pairs involved in restraints
1870 are written to the energy file (can make the energy file very
1877 ignore orientation restraint information in topology file
1881 use orientation restraints, ensemble averaging can be performed
1887 force constant for orientation restraints, which is multiplied by a
1888 (possibly) different weight factor for each restraint, can be set
1889 to zero to obtain the orientations from a free simulation
1894 time constant for orientation restraints running average. A value
1895 of zero turns off time averaging.
1897 .. mdp:: orire-fitgrp
1899 fit group for orientation restraining. This group of atoms is used
1900 to determine the rotation **R** of the system with respect to the
1901 reference orientation. The reference orientation is the starting
1902 conformation of the first subsystem. For a protein, backbone is a
1905 .. mdp:: nstorireout
1908 period between steps when the running time-averaged and
1909 instantaneous orientations for all restraints, and the molecular
1910 order tensor are written to the energy file (can make the energy
1914 Free energy calculations
1915 ^^^^^^^^^^^^^^^^^^^^^^^^
1917 .. mdp:: free-energy
1921 Only use topology A.
1925 Interpolate between topology A (lambda=0) to topology B
1926 (lambda=1) and write the derivative of the Hamiltonian with
1927 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
1928 or the Hamiltonian differences with respect to other lambda
1929 values (as specified with foreign lambda) to the energy file
1930 and/or to ``dhdl.xvg``, where they can be processed by, for
1931 example :ref:`gmx bar`. The potentials, bond-lengths and angles
1932 are interpolated linearly as described in the manual. When
1933 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
1934 used for the LJ and Coulomb interactions.
1938 Turns on expanded ensemble simulation, where the alchemical state
1939 becomes a dynamic variable, allowing jumping between different
1940 Hamiltonians. See the expanded ensemble options for controlling how
1941 expanded ensemble simulations are performed. The different
1942 Hamiltonians used in expanded ensemble simulations are defined by
1943 the other free energy options.
1945 .. mdp:: init-lambda
1948 starting value for lambda (float). Generally, this should only be
1949 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
1950 other cases, :mdp:`init-lambda-state` should be specified
1951 instead. Must be greater than or equal to 0.
1953 .. mdp:: delta-lambda
1956 increment per time step for lambda
1958 .. mdp:: init-lambda-state
1961 starting value for the lambda state (integer). Specifies which
1962 columm of the lambda vector (:mdp:`coul-lambdas`,
1963 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
1964 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
1965 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
1966 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
1967 the first column, and so on.
1969 .. mdp:: fep-lambdas
1972 Zero, one or more lambda values for which Delta H values will be
1973 determined and written to dhdl.xvg every :mdp:`nstdhdl`
1974 steps. Values must be between 0 and 1. Free energy differences
1975 between different lambda values can then be determined with
1976 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
1977 other -lambdas keywords because all components of the lambda vector
1978 that are not specified will use :mdp:`fep-lambdas` (including
1979 :mdp:`restraint-lambdas` and therefore the pull code restraints).
1981 .. mdp:: coul-lambdas
1984 Zero, one or more lambda values for which Delta H values will be
1985 determined and written to dhdl.xvg every :mdp:`nstdhdl`
1986 steps. Values must be between 0 and 1. Only the electrostatic
1987 interactions are controlled with this component of the lambda
1988 vector (and only if the lambda=0 and lambda=1 states have differing
1989 electrostatic interactions).
1991 .. mdp:: vdw-lambdas
1994 Zero, one or more lambda values for which Delta H values will be
1995 determined and written to dhdl.xvg every :mdp:`nstdhdl`
1996 steps. Values must be between 0 and 1. Only the van der Waals
1997 interactions are controlled with this component of the lambda
2000 .. mdp:: bonded-lambdas
2003 Zero, one or more lambda values for which Delta H values will be
2004 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2005 steps. Values must be between 0 and 1. Only the bonded interactions
2006 are controlled with this component of the lambda vector.
2008 .. mdp:: restraint-lambdas
2011 Zero, one or more lambda values for which Delta H values will be
2012 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2013 steps. Values must be between 0 and 1. Only the restraint
2014 interactions: dihedral restraints, and the pull code restraints are
2015 controlled with this component of the lambda vector.
2017 .. mdp:: mass-lambdas
2020 Zero, one or more lambda values for which Delta H values will be
2021 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2022 steps. Values must be between 0 and 1. Only the particle masses are
2023 controlled with this component of the lambda vector.
2025 .. mdp:: temperature-lambdas
2028 Zero, one or more lambda values for which Delta H values will be
2029 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2030 steps. Values must be between 0 and 1. Only the temperatures
2031 controlled with this component of the lambda vector. Note that
2032 these lambdas should not be used for replica exchange, only for
2033 simulated tempering.
2035 .. mdp:: calc-lambda-neighbors
2038 Controls the number of lambda values for which Delta H values will
2039 be calculated and written out, if :mdp:`init-lambda-state` has
2040 been set. A positive value will limit the number of lambda points
2041 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2042 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2043 has a value of 2, energies for lambda points 3-7 will be calculated
2044 and writen out. A value of -1 means all lambda points will be
2045 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2046 1 is sufficient, while for MBAR -1 should be used.
2051 the soft-core alpha parameter, a value of 0 results in linear
2052 interpolation of the LJ and Coulomb interactions
2057 the power of the radial term in the soft-core equation. Possible
2058 values are 6 and 48. 6 is more standard, and is the default. When
2059 48 is used, then sc-alpha should generally be much lower (between
2065 Whether to apply the soft-core free energy interaction
2066 transformation to the Columbic interaction of a molecule. Default
2067 is no, as it is generally more efficient to turn off the Coulomic
2068 interactions linearly before turning off the van der Waals
2069 interactions. Note that it is only taken into account when lambda
2070 states are used, not with :mdp:`couple-lambda0` /
2071 :mdp:`couple-lambda1`, and you can still turn off soft-core
2072 interactions by setting :mdp:`sc-alpha` to 0.
2077 the power for lambda in the soft-core function, only the values 1
2083 the soft-core sigma for particles which have a C6 or C12 parameter
2084 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2086 .. mdp:: couple-moltype
2088 Here one can supply a molecule type (as defined in the topology)
2089 for calculating solvation or coupling free energies. There is a
2090 special option ``system`` that couples all molecule types in the
2091 system. This can be useful for equilibrating a system starting from
2092 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2093 on. The Van der Waals interactions and/or charges in this molecule
2094 type can be turned on or off between lambda=0 and lambda=1,
2095 depending on the settings of :mdp:`couple-lambda0` and
2096 :mdp:`couple-lambda1`. If you want to decouple one of several
2097 copies of a molecule, you need to copy and rename the molecule
2098 definition in the topology.
2100 .. mdp:: couple-lambda0
2102 .. mdp-value:: vdw-q
2104 all interactions are on at lambda=0
2108 the charges are zero (no Coulomb interactions) at lambda=0
2112 the Van der Waals interactions are turned at lambda=0; soft-core
2113 interactions will be required to avoid singularities
2117 the Van der Waals interactions are turned off and the charges
2118 are zero at lambda=0; soft-core interactions will be required to
2119 avoid singularities.
2121 .. mdp:: couple-lambda1
2123 analogous to :mdp:`couple-lambda1`, but for lambda=1
2125 .. mdp:: couple-intramol
2129 All intra-molecular non-bonded interactions for moleculetype
2130 :mdp:`couple-moltype` are replaced by exclusions and explicit
2131 pair interactions. In this manner the decoupled state of the
2132 molecule corresponds to the proper vacuum state without
2133 periodicity effects.
2137 The intra-molecular Van der Waals and Coulomb interactions are
2138 also turned on/off. This can be useful for partitioning
2139 free-energies of relatively large molecules, where the
2140 intra-molecular non-bonded interactions might lead to
2141 kinetically trapped vacuum conformations. The 1-4 pair
2142 interactions are not turned off.
2147 the frequency for writing dH/dlambda and possibly Delta H to
2148 dhdl.xvg, 0 means no ouput, should be a multiple of
2149 :mdp:`nstcalcenergy`.
2151 .. mdp:: dhdl-derivatives
2155 If yes (the default), the derivatives of the Hamiltonian with
2156 respect to lambda at each :mdp:`nstdhdl` step are written
2157 out. These values are needed for interpolation of linear energy
2158 differences with :ref:`gmx bar` (although the same can also be
2159 achieved with the right foreign lambda setting, that may not be as
2160 flexible), or with thermodynamic integration
2162 .. mdp:: dhdl-print-energy
2166 Include either the total or the potential energy in the dhdl
2167 file. Options are 'no', 'potential', or 'total'. This information
2168 is needed for later free energy analysis if the states of interest
2169 are at different temperatures. If all states are at the same
2170 temperature, this information is not needed. 'potential' is useful
2171 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2172 file. When rerunning from an existing trajectory, the kinetic
2173 energy will often not be correct, and thus one must compute the
2174 residual free energy from the potential alone, with the kinetic
2175 energy component computed analytically.
2177 .. mdp:: separate-dhdl-file
2181 The free energy values that are calculated (as specified with
2182 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2183 written out to a separate file, with the default name
2184 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2189 The free energy values are written out to the energy output file
2190 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2191 steps), where they can be extracted with :ref:`gmx energy` or
2192 used directly with :ref:`gmx bar`.
2194 .. mdp:: dh-hist-size
2197 If nonzero, specifies the size of the histogram into which the
2198 Delta H values (specified with foreign lambda) and the derivative
2199 dH/dl values are binned, and written to ener.edr. This can be used
2200 to save disk space while calculating free energy differences. One
2201 histogram gets written for each foreign lambda and two for the
2202 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2203 histogram settings (too small size or too wide bins) can introduce
2204 errors. Do not use histograms unless you're certain you need it.
2206 .. mdp:: dh-hist-spacing
2209 Specifies the bin width of the histograms, in energy units. Used in
2210 conjunction with :mdp:`dh-hist-size`. This size limits the
2211 accuracy with which free energies can be calculated. Do not use
2212 histograms unless you're certain you need it.
2215 Expanded Ensemble calculations
2216 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2218 .. mdp:: nstexpanded
2220 The number of integration steps beween attempted moves changing the
2221 system Hamiltonian in expanded ensemble simulations. Must be a
2222 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2229 No Monte Carlo in state space is performed.
2231 .. mdp-value:: metropolis-transition
2233 Uses the Metropolis weights to update the expanded ensemble
2234 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2237 .. mdp-value:: barker-transition
2239 Uses the Barker transition critera to update the expanded
2240 ensemble weight of each state i, defined by exp(-beta_new
2241 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2243 .. mdp-value:: wang-landau
2245 Uses the Wang-Landau algorithm (in state space, not energy
2246 space) to update the expanded ensemble weights.
2248 .. mdp-value:: min-variance
2250 Uses the minimum variance updating method of Escobedo et al. to
2251 update the expanded ensemble weights. Weights will not be the
2252 free energies, but will rather emphasize states that need more
2253 sampling to give even uncertainty.
2255 .. mdp:: lmc-mc-move
2259 No Monte Carlo in state space is performed.
2261 .. mdp-value:: metropolis-transition
2263 Randomly chooses a new state up or down, then uses the
2264 Metropolis critera to decide whether to accept or reject:
2265 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2267 .. mdp-value:: barker-transition
2269 Randomly chooses a new state up or down, then uses the Barker
2270 transition critera to decide whether to accept or reject:
2271 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2273 .. mdp-value:: gibbs
2275 Uses the conditional weights of the state given the coordinate
2276 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2279 .. mdp-value:: metropolized-gibbs
2281 Uses the conditional weights of the state given the coordinate
2282 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2283 to move to, EXCLUDING the current state, then uses a rejection
2284 step to ensure detailed balance. Always more efficient that
2285 Gibbs, though only marginally so in many situations, such as
2286 when only the nearest neighbors have decent phase space
2292 random seed to use for Monte Carlo moves in state space. When
2293 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2295 .. mdp:: mc-temperature
2297 Temperature used for acceptance/rejection for Monte Carlo moves. If
2298 not specified, the temperature of the simulation specified in the
2299 first group of :mdp:`ref-t` is used.
2304 The cutoff for the histogram of state occupancies to be reset, and
2305 the free energy incrementor to be changed from delta to delta *
2306 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2307 each histogram) / (average number of samples at each
2308 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2309 histogram is only considered flat if all Nratio > 0.8 AND
2310 simultaneously all 1/Nratio > 0.8.
2315 Each time the histogram is considered flat, then the current value
2316 of the Wang-Landau incrementor for the free energies is multiplied
2317 by :mdp:`wl-scale`. Value must be between 0 and 1.
2319 .. mdp:: init-wl-delta
2322 The initial value of the Wang-Landau incrementor in kT. Some value
2323 near 1 kT is usually most efficient, though sometimes a value of
2324 2-3 in units of kT works better if the free energy differences are
2327 .. mdp:: wl-oneovert
2330 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2331 the large sample limit. There is significant evidence that the
2332 standard Wang-Landau algorithms in state space presented here
2333 result in free energies getting 'burned in' to incorrect values
2334 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2335 then when the incrementor becomes less than 1/N, where N is the
2336 mumber of samples collected (and thus proportional to the data
2337 collection time, hence '1 over t'), then the Wang-Lambda
2338 incrementor is set to 1/N, decreasing every step. Once this occurs,
2339 :mdp:`wl-ratio` is ignored, but the weights will still stop
2340 updating when the equilibration criteria set in
2341 :mdp:`lmc-weights-equil` is achieved.
2343 .. mdp:: lmc-repeats
2346 Controls the number of times that each Monte Carlo swap type is
2347 performed each iteration. In the limit of large numbers of Monte
2348 Carlo repeats, then all methods converge to Gibbs sampling. The
2349 value will generally not need to be different from 1.
2351 .. mdp:: lmc-gibbsdelta
2354 Limit Gibbs sampling to selected numbers of neighboring states. For
2355 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2356 sampling over all of the states that are defined. A positive value
2357 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2358 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2359 value of -1 means that all states are considered. For less than 100
2360 states, it is probably not that expensive to include all states.
2362 .. mdp:: lmc-forced-nstart
2365 Force initial state space sampling to generate weights. In order to
2366 come up with reasonable initial weights, this setting allows the
2367 simulation to drive from the initial to the final lambda state,
2368 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2369 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2370 sufficiently long (thousands of steps, perhaps), then the weights
2371 will be close to correct. However, in most cases, it is probably
2372 better to simply run the standard weight equilibration algorithms.
2374 .. mdp:: nst-transition-matrix
2377 Frequency of outputting the expanded ensemble transition matrix. A
2378 negative number means it will only be printed at the end of the
2381 .. mdp:: symmetrized-transition-matrix
2384 Whether to symmetrize the empirical transition matrix. In the
2385 infinite limit the matrix will be symmetric, but will diverge with
2386 statistical noise for short timescales. Forced symmetrization, by
2387 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2388 like the existence of (small magnitude) negative eigenvalues.
2390 .. mdp:: mininum-var-min
2393 The min-variance strategy (option of :mdp:`lmc-stats` is only
2394 valid for larger number of samples, and can get stuck if too few
2395 samples are used at each state. :mdp:`mininum-var-min` is the
2396 minimum number of samples that each state that are allowed before
2397 the min-variance strategy is activated if selected.
2399 .. mdp:: init-lambda-weights
2401 The initial weights (free energies) used for the expanded ensemble
2402 states. Default is a vector of zero weights. format is similar to
2403 the lambda vector settings in :mdp:`fep-lambdas`, except the
2404 weights can be any floating point number. Units are kT. Its length
2405 must match the lambda vector lengths.
2407 .. mdp:: lmc-weights-equil
2411 Expanded ensemble weights continue to be updated throughout the
2416 The input expanded ensemble weights are treated as equilibrated,
2417 and are not updated throughout the simulation.
2419 .. mdp-value:: wl-delta
2421 Expanded ensemble weight updating is stopped when the
2422 Wang-Landau incrementor falls below this value.
2424 .. mdp-value:: number-all-lambda
2426 Expanded ensemble weight updating is stopped when the number of
2427 samples at all of the lambda states is greater than this value.
2429 .. mdp-value:: number-steps
2431 Expanded ensemble weight updating is stopped when the number of
2432 steps is greater than the level specified by this value.
2434 .. mdp-value:: number-samples
2436 Expanded ensemble weight updating is stopped when the number of
2437 total samples across all lambda states is greater than the level
2438 specified by this value.
2440 .. mdp-value:: count-ratio
2442 Expanded ensemble weight updating is stopped when the ratio of
2443 samples at the least sampled lambda state and most sampled
2444 lambda state greater than this value.
2446 .. mdp:: simulated-tempering
2449 Turn simulated tempering on or off. Simulated tempering is
2450 implemented as expanded ensemble sampling with different
2451 temperatures instead of different Hamiltonians.
2453 .. mdp:: sim-temp-low
2456 Low temperature for simulated tempering.
2458 .. mdp:: sim-temp-high
2461 High temperature for simulated tempering.
2463 .. mdp:: simulated-tempering-scaling
2465 Controls the way that the temperatures at intermediate lambdas are
2466 calculated from the :mdp:`temperature-lambdas` part of the lambda
2469 .. mdp-value:: linear
2471 Linearly interpolates the temperatures using the values of
2472 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2473 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2474 a temperature of 350. A nonlinear set of temperatures can always
2475 be implemented with uneven spacing in lambda.
2477 .. mdp-value:: geometric
2479 Interpolates temperatures geometrically between
2480 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2481 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2482 :mdp:`sim-temp-low`) raised to the power of
2483 (i/(ntemps-1)). This should give roughly equal exchange for
2484 constant heat capacity, though of course things simulations that
2485 involve protein folding have very high heat capacity peaks.
2487 .. mdp-value:: exponential
2489 Interpolates temperatures exponentially between
2490 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2491 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2492 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2493 (i))-1)/(exp(1.0)-i)).
2501 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2502 in groups Protein and Sol will experience constant acceleration as
2503 specified in the :mdp:`accelerate` line
2508 acceleration for :mdp:`acc-grps`; x, y and z for each group
2509 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2510 constant acceleration of 0.1 nm ps-2 in X direction, second group
2515 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2516 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2517 specifies for which dimension the freezing applies. To avoid
2518 spurious contibrutions to the virial and pressure due to large
2519 forces between completely frozen atoms you need to use energy group
2520 exclusions, this also saves computing time. Note that coordinates
2521 of frozen atoms are not scaled by pressure-coupling algorithms.
2525 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2526 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
2527 N N N N`` means that particles in the first group can move only in
2528 Z direction. The particles in the second group can move in any
2531 .. mdp:: cos-acceleration
2534 the amplitude of the acceleration profile for calculating the
2535 viscosity. The acceleration is in the X-direction and the magnitude
2536 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2537 added to the energy file: the amplitude of the velocity profile and
2542 (0 0 0 0 0 0) \[nm ps-1\]
2543 The velocities of deformation for the box elements: a(x) b(y) c(z)
2544 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2545 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2546 elements are corrected for periodicity. The coordinates are
2547 transformed accordingly. Frozen degrees of freedom are (purposely)
2548 also transformed. The time ts is set to t at the first step and at
2549 steps at which x and v are written to trajectory to ensure exact
2550 restarts. Deformation can be used together with semiisotropic or
2551 anisotropic pressure coupling when the appropriate
2552 compressibilities are set to zero. The diagonal elements can be
2553 used to strain a solid. The off-diagonal elements can be used to
2554 shear a solid or a liquid.
2560 .. mdp:: E-x ; E-y ; E-z
2562 If you want to use an electric field in a direction, enter 3
2563 numbers after the appropriate E-direction, the first number: the
2564 number of cosines, only 1 is implemented (with frequency 0) so
2565 enter 1, the second number: the strength of the electric field in V
2566 nm^-1, the third number: the phase of the cosine, you can enter any
2567 number here since a cosine of frequency zero has no phase.
2569 .. mdp:: E-xt; E-yt; E-zt
2571 Here you can specify a pulsed alternating electric field. The field
2572 has the form of a gaussian laser pulse:
2574 E(t) = E0 exp ( -(t-t0)^2/(2 sigma^2) ) cos(omega (t-t0))
2576 For example, the four parameters for direction x are set in the
2577 three fields of :mdp:`E-x` and :mdp:`E-xt` like
2581 E-xt = omega t0 sigma
2583 In the special case that sigma = 0, the exponential term is omitted
2584 and only the cosine term is used.
2586 More details in Carl Caleman and David van der Spoel: Picosecond
2587 Melting of Ice by an Infrared Laser Pulse - A Simulation Study
2588 Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008)
2592 Mixed quantum/classical molecular dynamics
2593 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2603 Do a QM/MM simulation. Several groups can be described at
2604 different QM levels separately. These are specified in the
2605 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
2606 initio* theory at which the groups are described is specified by
2607 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
2608 groups at different levels of theory is only possible with the
2609 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
2613 groups to be descibed at the QM level
2617 .. mdp-value:: normal
2619 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
2620 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
2621 *ab initio* theory. The rest of the system is described at the
2622 MM level. The QM and MM subsystems interact as follows: MM point
2623 charges are included in the QM one-electron hamiltonian and all
2624 Lennard-Jones interactions are described at the MM level.
2626 .. mdp-value:: ONIOM
2628 The interaction between the subsystem is described using the
2629 ONIOM method by Morokuma and co-workers. There can be more than
2630 one :mdp:`QMMM-grps` each modeled at a different level of QM
2631 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
2636 Method used to compute the energy and gradients on the QM
2637 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
2638 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
2639 included in the active space is specified by :mdp:`CASelectrons`
2640 and :mdp:`CASorbitals`.
2645 Basis set used to expand the electronic wavefuntion. Only Gaussian
2646 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
2647 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
2652 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
2653 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
2654 layer needs to be specified separately.
2659 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
2660 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
2661 needs to be specified separately.
2663 .. mdp:: CASorbitals
2666 The number of orbitals to be included in the active space when
2667 doing a CASSCF computation.
2669 .. mdp:: CASelectrons
2672 The number of electrons to be included in the active space when
2673 doing a CASSCF computation.
2679 No surface hopping. The system is always in the electronic
2684 Do a QM/MM MD simulation on the excited state-potential energy
2685 surface and enforce a *diabatic* hop to the ground-state when
2686 the system hits the conical intersection hyperline in the course
2687 the simulation. This option only works in combination with the
2694 .. mdp:: implicit-solvent
2702 Do a simulation with implicit solvent using the Generalized Born
2703 formalism. Three different methods for calculating the Born
2704 radii are available, Still, HCT and OBC. These are specified
2705 with the :mdp:`gb-algorithm` field. The non-polar solvation is
2706 specified with the :mdp:`sa-algorithm` field.
2708 .. mdp:: gb-algorithm
2710 .. mdp-value:: Still
2712 Use the Still method to calculate the Born radii
2716 Use the Hawkins-Cramer-Truhlar method to calculate the Born
2721 Use the Onufriev-Bashford-Case method to calculate the Born
2727 Frequency to (re)-calculate the Born radii. For most practial
2728 purposes, setting a value larger than 1 violates energy
2729 conservation and leads to unstable trajectories.
2734 Cut-off for the calculation of the Born radii. Currently must be
2737 .. mdp:: gb-epsilon-solvent
2740 Dielectric constant for the implicit solvent
2742 .. mdp:: gb-saltconc
2745 Salt concentration for implicit solvent models, currently not used
2747 .. mdp:: gb-obc-alpha
2748 .. mdp:: gb-obc-beta
2749 .. mdp:: gb-obc-gamma
2751 Scale factors for the OBC model. Default values of 1, 0.78 and 4.85
2752 respectively are for OBC(II). Values for OBC(I) are 0.8, 0 and 2.91
2755 .. mdp:: gb-dielectric-offset
2758 Distance for the di-electric offset when calculating the Born
2759 radii. This is the offset between the center of each atom the
2760 center of the polarization energy for the corresponding atom
2762 .. mdp:: sa-algorithm
2764 .. mdp-value:: Ace-approximation
2766 Use an Ace-type approximation
2770 No non-polar solvation calculation done. For GBSA only the polar
2771 part gets calculated
2773 .. mdp:: sa-surface-tension
2776 Default value for surface tension with SA algorithms. The default
2777 value is -1; Note that if this default value is not changed it will
2778 be overridden by :ref:`gmx grompp` using values that are specific
2779 for the choice of radii algorithm (0.0049 kcal/mol/Angstrom^2 for
2780 Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will
2781 while using an sa-algorithm other than None means no non-polar
2782 calculations are done.
2785 Computational Electrophysiology
2786 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2787 Use these options to switch on and control ion/water position exchanges in "Computational
2788 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
2794 Do not enable ion/water position exchanges.
2796 .. mdp-value:: X ; Y ; Z
2798 Allow for ion/water position exchanges along the chosen direction.
2799 In a typical setup with the membranes parallel to the x-y plane,
2800 ion/water pairs need to be exchanged in Z direction to sustain the
2801 requested ion concentrations in the compartments.
2803 .. mdp:: swap-frequency
2805 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
2806 per compartment are determined and exchanges made if necessary.
2807 Normally it is not necessary to check at every time step.
2808 For typical Computational Electrophysiology setups, a value of about 100 is
2809 sufficient and yields a negligible performance impact.
2811 .. mdp:: split-group0
2813 Name of the index group of the membrane-embedded part of channel #0.
2814 The center of mass of these atoms defines one of the compartment boundaries
2815 and should be chosen such that it is near the center of the membrane.
2817 .. mdp:: split-group1
2819 Channel #1 defines the position of the other compartment boundary.
2821 .. mdp:: massw-split0
2823 (no) Defines whether or not mass-weighting is used to calculate the split group center.
2827 Use the geometrical center.
2831 Use the center of mass.
2833 .. mdp:: massw-split1
2835 (no) As above, but for split-group #1.
2837 .. mdp:: solvent-group
2839 Name of the index group of solvent molecules.
2841 .. mdp:: coupl-steps
2843 (\10) Average the number of ions per compartment over these many swap attempt steps.
2844 This can be used to prevent that ions near a compartment boundary
2845 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
2849 (1) The number of different ion types to be controlled. These are during the
2850 simulation exchanged with solvent molecules to reach the desired reference numbers.
2852 .. mdp:: iontype0-name
2854 Name of the first ion type.
2856 .. mdp:: iontype0-in-A
2858 (-1) Requested (=reference) number of ions of type 0 in compartment A.
2859 The default value of -1 means: use the number of ions as found in time step 0
2862 .. mdp:: iontype0-in-B
2864 (-1) Reference number of ions of type 0 for compartment B.
2866 .. mdp:: bulk-offsetA
2868 (0.0) Offset of the first swap layer from the compartment A midplane.
2869 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
2870 at maximum distance (= bulk concentration) to the split group layers. However,
2871 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
2872 towards one of the compartment-partitioning layers (at +/- 1.0).
2874 .. mdp:: bulk-offsetB
2876 (0.0) Offset of the other swap layer from the compartment B midplane.
2881 (\1) Only swap ions if threshold difference to requested count is reached.
2885 (2.0) \[nm\] Radius of the split cylinder #0.
2886 Two split cylinders (mimicking the channel pores) can optionally be defined
2887 relative to the center of the split group. With the help of these cylinders
2888 it can be counted which ions have passed which channel. The split cylinder
2889 definition has no impact on whether or not ion/water swaps are done.
2893 (1.0) \[nm\] Upper extension of the split cylinder #0.
2897 (1.0) \[nm\] Lower extension of the split cylinder #0.
2901 (2.0) \[nm\] Radius of the split cylinder #1.
2905 (1.0) \[nm\] Upper extension of the split cylinder #1.
2909 (1.0) \[nm\] Lower extension of the split cylinder #1.
2912 User defined thingies
2913 ^^^^^^^^^^^^^^^^^^^^^
2917 .. mdp:: userint1 (0)
2918 .. mdp:: userint2 (0)
2919 .. mdp:: userint3 (0)
2920 .. mdp:: userint4 (0)
2921 .. mdp:: userreal1 (0)
2922 .. mdp:: userreal2 (0)
2923 .. mdp:: userreal3 (0)
2924 .. mdp:: userreal4 (0)
2926 These you can use if you modify code. You can pass integers and
2927 reals and groups to your subroutine. Check the inputrec definition
2928 in ``src/gromacs/mdtypes/inputrec.h``
2933 This feature has been removed from |Gromacs|, but so that old
2934 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
2935 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
2936 fatal error if this is set.
2942 .. _reference manual: gmx-manual-parent-dir_
biod.pnpi.spb.ru / alexxy / gromacs.git / blob