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.
7 .. todo:: Make more cross-references.
9 Molecular dynamics parameters (.mdp options)
10 ============================================
17 Default values are given in parentheses, or listed first among
18 choices. The first option in the list is always the default
19 option. Units are given in square brackets. The difference between a
20 dash and an underscore is ignored.
22 A :ref:`sample mdp file <mdp>` is available. This should be
23 appropriate to start a normal simulation. Edit it to suit your
24 specific needs and desires.
32 directories to include in your topology. Format:
33 ``-I/home/john/mylib -I../otherlib``
37 defines to pass to the preprocessor, default is no defines. You can
38 use any defines to control options in your customized topology
39 files. Options that act on existing :ref:`top` file mechanisms
42 ``-DFLEXIBLE`` will use flexible water instead of rigid water
43 into your topology, this can be useful for normal mode analysis.
45 ``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
46 your topology, used for implementing position restraints.
54 (Despite the name, this list includes algorithms that are not
55 actually integrators over time. :mdp-value:`integrator=steep` and
56 all entries following it are in this category)
60 A leap-frog algorithm for integrating Newton's equations of motion.
64 A velocity Verlet algorithm for integrating Newton's equations
65 of motion. For constant NVE simulations started from
66 corresponding points in the same trajectory, the trajectories
67 are analytically, but not binary, identical to the
68 :mdp-value:`integrator=md` leap-frog integrator. The kinetic
69 energy, which is determined from the whole step velocities and
70 is therefore slightly too high. The advantage of this integrator
71 is more accurate, reversible Nose-Hoover and Parrinello-Rahman
72 coupling integration based on Trotter expansion, as well as
73 (slightly too small) full step velocity output. This all comes
74 at the cost off extra computation, especially with constraints
75 and extra communication in parallel. Note that for nearly all
76 production simulations the :mdp-value:`integrator=md` integrator
79 .. mdp-value:: md-vv-avek
81 A velocity Verlet algorithm identical to
82 :mdp-value:`integrator=md-vv`, except that the kinetic energy is
83 determined as the average of the two half step kinetic energies
84 as in the :mdp-value:`integrator=md` integrator, and this thus
85 more accurate. With Nose-Hoover and/or Parrinello-Rahman
86 coupling this comes with a slight increase in computational
91 An accurate and efficient leap-frog stochastic dynamics
92 integrator. With constraints, coordinates needs to be
93 constrained twice per integration step. Depending on the
94 computational cost of the force calculation, this can take a
95 significant part of the simulation time. The temperature for one
96 or more groups of atoms (:mdp:`tc-grps`) is set with
97 :mdp:`ref-t`, the inverse friction constant for each group is
98 set with :mdp:`tau-t`. The parameters :mdp:`tcoupl` and :mdp:`nsttcouple`
99 are ignored. The random generator is initialized with
100 :mdp:`ld-seed`. When used as a thermostat, an appropriate value
101 for :mdp:`tau-t` is 2 ps, since this results in a friction that
102 is lower than the internal friction of water, while it is high
103 enough to remove excess heat NOTE: temperature deviations decay
104 twice as fast as with a Berendsen thermostat with the same
109 An Euler integrator for Brownian or position Langevin dynamics,
110 the velocity is the force divided by a friction coefficient
111 (:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
112 :mdp:`bd-fric` is 0, the friction coefficient for each particle
113 is calculated as mass/ :mdp:`tau-t`, as for the integrator
114 :mdp-value:`integrator=sd`. The random generator is initialized
119 A steepest descent algorithm for energy minimization. The
120 maximum step size is :mdp:`emstep`, the tolerance is
125 A conjugate gradient algorithm for energy minimization, the
126 tolerance is :mdp:`emtol`. CG is more efficient when a steepest
127 descent step is done every once in a while, this is determined
128 by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
129 analysis, which requires a very high accuracy, |Gromacs| should be
130 compiled in double precision.
132 .. mdp-value:: l-bfgs
134 A quasi-Newtonian algorithm for energy minimization according to
135 the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
136 practice this seems to converge faster than Conjugate Gradients,
137 but due to the correction steps necessary it is not (yet)
142 Normal mode analysis is performed on the structure in the :ref:`tpr`
143 file. |Gromacs| should be compiled in double precision.
147 Test particle insertion. The last molecule in the topology is
148 the test particle. A trajectory must be provided to ``mdrun
149 -rerun``. This trajectory should not contain the molecule to be
150 inserted. Insertions are performed :mdp:`nsteps` times in each
151 frame at random locations and with random orientiations of the
152 molecule. When :mdp:`nstlist` is larger than one,
153 :mdp:`nstlist` insertions are performed in a sphere with radius
154 :mdp:`rtpi` around a the same random location using the same
155 pair list. Since pair list construction is expensive,
156 one can perform several extra insertions with the same list
157 almost for free. The random seed is set with
158 :mdp:`ld-seed`. The temperature for the Boltzmann weighting is
159 set with :mdp:`ref-t`, this should match the temperature of the
160 simulation of the original trajectory. Dispersion correction is
161 implemented correctly for TPI. All relevant quantities are
162 written to the file specified with ``mdrun -tpi``. The
163 distribution of insertion energies is written to the file
164 specified with ``mdrun -tpid``. No trajectory or energy file is
165 written. Parallel TPI gives identical results to single-node
166 TPI. For charged molecules, using PME with a fine grid is most
167 accurate and also efficient, since the potential in the system
168 only needs to be calculated once per frame.
172 Test particle insertion into a predefined cavity location. The
173 procedure is the same as for :mdp-value:`integrator=tpi`, except
174 that one coordinate extra is read from the trajectory, which is
175 used as the insertion location. The molecule to be inserted
176 should be centered at 0,0,0. |Gromacs| does not do this for you,
177 since for different situations a different way of centering
178 might be optimal. Also :mdp:`rtpi` sets the radius for the
179 sphere around this location. Neighbor searching is done only
180 once per frame, :mdp:`nstlist` is not used. Parallel
181 :mdp-value:`integrator=tpic` gives identical results to
182 single-rank :mdp-value:`integrator=tpic`.
186 Enable MiMiC QM/MM coupling to run hybrid molecular dynamics.
187 Keey in mind that its required to launch CPMD compiled with MiMiC as well.
188 In this mode all options regarding integration (T-coupling, P-coupling,
189 timestep and number of steps) are ignored as CPMD will do the integration
190 instead. Options related to forces computation (cutoffs, PME parameters,
191 etc.) are working as usual. Atom selection to define QM atoms is read
192 from :mdp:`QMMM-grps`
197 starting time for your run (only makes sense for time-based
203 time step for integration (only makes sense for time-based
209 maximum number of steps to integrate or minimize, -1 is no
215 The starting step. The time at step i in a run is
216 calculated as: t = :mdp:`tinit` + :mdp:`dt` *
217 (:mdp:`init-step` + i). The free-energy lambda is calculated
218 as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
219 (:mdp:`init-step` + i). Also non-equilibrium MD parameters can
220 depend on the step number. Thus for exact restarts or redoing
221 part of a run it might be necessary to set :mdp:`init-step` to
222 the step number of the restart frame. :ref:`gmx convert-tpr`
223 does this automatically.
225 .. mdp:: simulation-part
228 A simulation can consist of multiple parts, each of which has
229 a part number. This option specifies what that number will
230 be, which helps keep track of parts that are logically the
231 same simulation. This option is generally useful to set only
232 when coping with a crashed simulation where files were lost.
238 Evaluate all forces at every integration step.
242 Use a multiple timing-stepping integrator to evaluate some forces, as specified
243 by :mdp:`mts-level2-forces` every :mdp:`mts-level2-factor` integration
244 steps. All other forces are evaluated at every step. MTS is currently
245 only supported with :mdp-value:`integrator=md`.
250 The number of levels for the multiple time-stepping scheme.
251 Currently only 2 is supported.
253 .. mdp:: mts-level2-forces
255 (longrange-nonbonded)
256 A list of one or more force groups that will be evaluated only every
257 :mdp:`mts-level2-factor` steps. Supported entries are:
258 ``longrange-nonbonded``, ``nonbonded``, ``pair``, ``dihedral``, ``angle``,
259 ``pull`` and ``awh``. With ``pair`` the listed pair forces (such as 1-4)
260 are selected. With ``dihedral`` all dihedrals are selected, including cmap.
261 All other forces, including all restraints, are evaluated and
262 integrated every step. When PME or Ewald is used for electrostatics
263 and/or LJ interactions, ``longrange-nonbonded`` can not be omitted here.
265 .. mdp:: mts-level2-factor
268 Interval for computing the forces in level 2 of the multiple time-stepping
273 .. mdp-value:: Linear
275 Remove center of mass translational velocity
277 .. mdp-value:: Angular
279 Remove center of mass translational and rotational velocity
281 .. mdp-value:: Linear-acceleration-correction
283 Remove center of mass translational velocity. Correct the center of
284 mass position assuming linear acceleration over :mdp:`nstcomm` steps.
285 This is useful for cases where an acceleration is expected on the
286 center of mass which is nearly constant over :mdp:`nstcomm` steps.
287 This can occur for example when pulling on a group using an absolute
292 No restriction on the center of mass motion
297 frequency for center of mass motion removal
301 group(s) for center of mass motion removal, default is the whole
310 (0) [amu ps\ :sup:`-1`]
311 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
312 the friction coefficient for each particle is calculated as mass/
318 used to initialize random generator for thermal noise for
319 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
320 a pseudo random seed is used. When running BD or SD on multiple
321 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
322 the processor number.
330 (10.0) [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
331 the minimization is converged when the maximum force is smaller
342 frequency of performing 1 steepest descent step while doing
343 conjugate gradient energy minimization.
348 Number of correction steps to use for L-BFGS minimization. A higher
349 number is (at least theoretically) more accurate, but slower.
352 Shell Molecular Dynamics
353 ^^^^^^^^^^^^^^^^^^^^^^^^
355 When shells or flexible constraints are present in the system the
356 positions of the shells and the lengths of the flexible constraints
357 are optimized at every time step until either the RMS force on the
358 shells and constraints is less than :mdp:`emtol`, or a maximum number
359 of iterations :mdp:`niter` has been reached. Minimization is converged
360 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
361 value should be 1.0 at most.
366 maximum number of iterations for optimizing the shell positions and
367 the flexible constraints.
372 the step size for optimizing the flexible constraints. Should be
373 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
374 particles in a flexible constraint and d2V/dq2 is the second
375 derivative of the potential in the constraint direction. Hopefully
376 this number does not differ too much between the flexible
377 constraints, as the number of iterations and thus the runtime is
378 very sensitive to fcstep. Try several values!
381 Test particle insertion
382 ^^^^^^^^^^^^^^^^^^^^^^^
387 the test particle insertion radius, see integrators
388 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
397 number of steps that elapse between writing coordinates to the output
398 trajectory file (:ref:`trr`), the last coordinates are always written
399 unless 0, which means coordinates are not written into the trajectory
405 number of steps that elapse between writing velocities to the output
406 trajectory file (:ref:`trr`), the last velocities are always written
407 unless 0, which means velocities are not written into the trajectory
413 number of steps that elapse between writing forces to the output
414 trajectory file (:ref:`trr`), the last forces are always written,
415 unless 0, which means forces are not written into the trajectory
421 number of steps that elapse between writing energies to the log
422 file, the last energies are always written.
424 .. mdp:: nstcalcenergy
427 number of steps that elapse between calculating the energies, 0 is
428 never. This option is only relevant with dynamics. This option affects the
429 performance in parallel simulations, because calculating energies
430 requires global communication between all processes which can
431 become a bottleneck at high parallelization.
436 number of steps that elapse between writing energies to energy file,
437 the last energies are always written, should be a multiple of
438 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
439 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
440 energy file, so :ref:`gmx energy` can report exact energy averages
441 and fluctuations also when :mdp:`nstenergy` > 1
443 .. mdp:: nstxout-compressed
446 number of steps that elapse between writing position coordinates
447 using lossy compression (:ref:`xtc` file), 0 for not writing
448 compressed coordinates output.
450 .. mdp:: compressed-x-precision
453 precision with which to write to the compressed trajectory file
455 .. mdp:: compressed-x-grps
457 group(s) to write to the compressed trajectory file, by default the
458 whole system is written (if :mdp:`nstxout-compressed` > 0)
462 group(s) for which to write to write short-ranged non-bonded
463 potential energies to the energy file (not supported on GPUs)
469 .. mdp:: cutoff-scheme
471 .. mdp-value:: Verlet
473 Generate a pair list with buffering. The buffer size is
474 automatically set based on :mdp:`verlet-buffer-tolerance`,
475 unless this is set to -1, in which case :mdp:`rlist` will be
480 Generate a pair list for groups of atoms, corresponding
481 to the charge groups in the topology. This option is no longer
490 Frequency to update the neighbor list. When dynamics and
491 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
492 a minimum value and :ref:`gmx mdrun` might increase it, unless
493 it is set to 1. With parallel simulations and/or non-bonded
494 force calculation on the GPU, a value of 20 or 40 often gives
495 the best performance. With energy minimization this parameter
496 is not used as the pair list is updated when at least one atom
497 has moved by more than half the pair list buffer size.
501 The neighbor list is only constructed once and never
502 updated. This is mainly useful for vacuum simulations in which
503 all particles see each other. But vacuum simulations are
504 (temporarily) not supported.
514 Use periodic boundary conditions in all directions.
518 Use no periodic boundary conditions, ignore the box. To simulate
519 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
520 best performance without cut-offs on a single MPI rank, set
521 :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`.
525 Use periodic boundary conditions in x and y directions
526 only. This works only with :mdp-value:`ns-type=grid` and can be used
527 in combination with walls_. Without walls or with only one wall
528 the system size is infinite in the z direction. Therefore
529 pressure coupling or Ewald summation methods can not be
530 used. These disadvantages do not apply when two walls are used.
532 .. mdp:: periodic-molecules
536 molecules are finite, fast molecular PBC can be used
540 for systems with molecules that couple to themselves through the
541 periodic boundary conditions, this requires a slower PBC
542 algorithm and molecules are not made whole in the output
544 .. mdp:: verlet-buffer-tolerance
546 (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
548 Used when performing a simulation with dynamics. This sets
549 the maximum allowed error for pair interactions per particle caused
550 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
551 :mdp:`nstlist` and the Verlet buffer size are fixed (for
552 performance reasons), particle pairs not in the pair list can
553 occasionally get within the cut-off distance during
554 :mdp:`nstlist` -1 steps. This causes very small jumps in the
555 energy. In a constant-temperature ensemble, these very small energy
556 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
557 estimate assumes a homogeneous particle distribution, hence the
558 errors might be slightly underestimated for multi-phase
559 systems. (See the `reference manual`_ for details). For longer
560 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
561 overestimated, because the interactions between particles are
562 ignored. Combined with cancellation of errors, the actual drift of
563 the total energy is usually one to two orders of magnitude
564 smaller. Note that the generated buffer size takes into account
565 that the |Gromacs| pair-list setup leads to a reduction in the
566 drift by a factor 10, compared to a simple particle-pair based
567 list. Without dynamics (energy minimization etc.), the buffer is 5%
568 of the cut-off. For NVE simulations the initial temperature is
569 used, unless this is zero, in which case a buffer of 10% is
570 used. For NVE simulations the tolerance usually needs to be lowered
571 to achieve proper energy conservation on the nanosecond time
572 scale. To override the automated buffer setting, use
573 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
578 Cut-off distance for the short-range neighbor list. With dynamics,
579 this is by default set by the :mdp:`verlet-buffer-tolerance` option
580 and the value of :mdp:`rlist` is ignored. Without dynamics, this
581 is by default set to the maximum cut-off plus 5% buffer, except
582 for test particle insertion, where the buffer is managed exactly
583 and automatically. For NVE simulations, where the automated
584 setting is not possible, the advised procedure is to run :ref:`gmx grompp`
585 with an NVT setup with the expected temperature and copy the resulting
586 value of :mdp:`rlist` to the NVE setup.
594 .. mdp-value:: Cut-off
596 Plain cut-off with pair list radius :mdp:`rlist` and
597 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
602 Classical Ewald sum electrostatics. The real-space cut-off
603 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
604 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
605 of wave vectors used in reciprocal space is controlled by
606 :mdp:`fourierspacing`. The relative accuracy of
607 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
609 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
610 large systems. It is included mainly for reference - in most
611 cases PME will perform much better.
615 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
616 space is similar to the Ewald sum, while the reciprocal part is
617 performed with FFTs. Grid dimensions are controlled with
618 :mdp:`fourierspacing` and the interpolation order with
619 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
620 interpolation the electrostatic forces have an accuracy of
621 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
622 this you might try 0.15 nm. When running in parallel the
623 interpolation parallelizes better than the FFT, so try
624 decreasing grid dimensions while increasing interpolation.
626 .. mdp-value:: P3M-AD
628 Particle-Particle Particle-Mesh algorithm with analytical
629 derivative for for long range electrostatic interactions. The
630 method and code is identical to SPME, except that the influence
631 function is optimized for the grid. This gives a slight increase
634 .. mdp-value:: Reaction-Field
636 Reaction field electrostatics with Coulomb cut-off
637 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
638 dielectric constant beyond the cut-off is
639 :mdp:`epsilon-rf`. The dielectric constant can be set to
640 infinity by setting :mdp:`epsilon-rf` =0.
644 Currently unsupported.
645 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
646 with user-defined potential functions for repulsion, dispersion
647 and Coulomb. When pair interactions are present, :ref:`gmx
648 mdrun` also expects to find a file ``tablep.xvg`` for the pair
649 interactions. When the same interactions should be used for
650 non-bonded and pair interactions the user can specify the same
651 file name for both table files. These files should contain 7
652 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
653 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
654 function, ``g(x)`` the dispersion function and ``h(x)`` the
655 repulsion function. When :mdp:`vdwtype` is not set to User the
656 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
657 the non-bonded interactions ``x`` values should run from 0 to
658 the largest cut-off distance + :mdp:`table-extension` and
659 should be uniformly spaced. For the pair interactions the table
660 length in the file will be used. The optimal spacing, which is
661 used for non-user tables, is ``0.002 nm`` when you run in mixed
662 precision or ``0.0005 nm`` when you run in double precision. The
663 function value at ``x=0`` is not important. More information is
664 in the printed manual.
666 .. mdp-value:: PME-Switch
668 Currently unsupported.
669 A combination of PME and a switch function for the direct-space
670 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
673 .. mdp-value:: PME-User
675 Currently unsupported.
676 A combination of PME and user tables (see
677 above). :mdp:`rcoulomb` is allowed to be smaller than
678 :mdp:`rlist`. The PME mesh contribution is subtracted from the
679 user table by :ref:`gmx mdrun`. Because of this subtraction the
680 user tables should contain about 10 decimal places.
682 .. mdp-value:: PME-User-Switch
684 Currently unsupported.
685 A combination of PME-User and a switching function (see
686 above). The switching function is applied to final
687 particle-particle interaction, *i.e.* both to the user supplied
688 function and the PME Mesh correction part.
690 .. mdp:: coulomb-modifier
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. This can be useful
702 when comparing energies with those computed with other software.
704 .. mdp:: rcoulomb-switch
707 where to start switching the Coulomb potential, only relevant
708 when force or potential switching is used
713 The distance for the Coulomb cut-off. Note that with PME this value
714 can be increased by the PME tuning in :ref:`gmx mdrun` along with
715 the PME grid spacing.
720 The relative dielectric constant. A value of 0 means infinity.
725 The relative dielectric constant of the reaction field. This
726 is only used with reaction-field electrostatics. A value of 0
735 .. mdp-value:: Cut-off
737 Plain cut-off with pair list radius :mdp:`rlist` and VdW
738 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
742 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
743 grid dimensions are controlled with :mdp:`fourierspacing` in
744 the same way as for electrostatics, and the interpolation order
745 is controlled with :mdp:`pme-order`. The relative accuracy of
746 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
747 and the specific combination rules that are to be used by the
748 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
752 This functionality is deprecated and replaced by using
753 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
754 The LJ (not Buckingham) potential is decreased over the whole range and
755 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
758 .. mdp-value:: Switch
760 This functionality is deprecated and replaced by using
761 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
762 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
763 which it is switched off to reach zero at :mdp:`rvdw`. Both the
764 potential and force functions are continuously smooth, but be
765 aware that all switch functions will give rise to a bulge
766 (increase) in the force (since we are switching the
771 Currently unsupported.
772 See user for :mdp:`coulombtype`. The function value at zero is
773 not important. When you want to use LJ correction, make sure
774 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
775 function. When :mdp:`coulombtype` is not set to User the values
776 for the ``f`` and ``-f'`` columns are ignored.
778 .. mdp:: vdw-modifier
780 .. mdp-value:: Potential-shift
782 Shift the Van der Waals potential by a constant such that it is
783 zero at the cut-off. This makes the potential the integral of
784 the force. Note that this does not affect the forces or the
789 Use an unmodified Van der Waals potential. This can be useful
790 when comparing energies with those computed with other software.
792 .. mdp-value:: Force-switch
794 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
795 and :mdp:`rvdw`. This shifts the potential shift over the whole
796 range and switches it to zero at the cut-off. Note that this is
797 more expensive to calculate than a plain cut-off and it is not
798 required for energy conservation, since Potential-shift
799 conserves energy just as well.
801 .. mdp-value:: Potential-switch
803 Smoothly switches the potential to zero between
804 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
805 articifically large forces in the switching region and is much
806 more expensive to calculate. This option should only be used if
807 the force field you are using requires this.
812 where to start switching the LJ force and possibly the potential,
813 only relevant when force or potential switching is used
818 distance for the LJ or Buckingham cut-off
824 don't apply any correction
826 .. mdp-value:: EnerPres
828 apply long range dispersion corrections for Energy and Pressure
832 apply long range dispersion corrections for Energy only
838 .. mdp:: table-extension
841 Extension of the non-bonded potential lookup tables beyond the
842 largest cut-off distance. With actual non-bonded interactions
843 the tables are never accessed beyond the cut-off. But a longer
844 table length might be needed for the 1-4 interactions, which
845 are always tabulated irrespective of the use of tables for
846 the non-bonded interactions.
848 .. mdp:: energygrp-table
850 Currently unsupported.
851 When user tables are used for electrostatics and/or VdW, here one
852 can give pairs of energy groups for which separate user tables
853 should be used. The two energy groups will be appended to the table
854 file name, in order of their definition in :mdp:`energygrps`,
855 separated by underscores. For example, if ``energygrps = Na Cl
856 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
857 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
858 normal ``table.xvg`` which will be used for all other energy group
865 .. mdp:: fourierspacing
868 For ordinary Ewald, the ratio of the box dimensions and the spacing
869 determines a lower bound for the number of wave vectors to use in
870 each (signed) direction. For PME and P3M, that ratio determines a
871 lower bound for the number of Fourier-space grid points that will
872 be used along that axis. In all cases, the number for each
873 direction can be overridden by entering a non-zero value for that
874 :mdp:`fourier-nx` direction. For optimizing the relative load of
875 the particle-particle interactions and the mesh part of PME, it is
876 useful to know that the accuracy of the electrostatics remains
877 nearly constant when the Coulomb cut-off and the PME grid spacing
878 are scaled by the same factor. Note that this spacing can be scaled
879 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
886 Highest magnitude of wave vectors in reciprocal space when using Ewald.
887 Grid size when using PME or P3M. These values override
888 :mdp:`fourierspacing` per direction. The best choice is powers of
889 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
890 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
896 Interpolation order for PME. 4 equals cubic interpolation. You
897 might try 6/8/10 when running in parallel and simultaneously
898 decrease grid dimension.
903 The relative strength of the Ewald-shifted direct potential at
904 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
905 will give a more accurate direct sum, but then you need more wave
906 vectors for the reciprocal sum.
908 .. mdp:: ewald-rtol-lj
911 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
912 to control the relative strength of the dispersion potential at
913 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
914 electrostatic potential.
916 .. mdp:: lj-pme-comb-rule
919 The combination rules used to combine VdW-parameters in the
920 reciprocal part of LJ-PME. Geometric rules are much faster than
921 Lorentz-Berthelot and usually the recommended choice, even when the
922 rest of the force field uses the Lorentz-Berthelot rules.
924 .. mdp-value:: Geometric
926 Apply geometric combination rules
928 .. mdp-value:: Lorentz-Berthelot
930 Apply Lorentz-Berthelot combination rules
932 .. mdp:: ewald-geometry
936 The Ewald sum is performed in all three dimensions.
940 The reciprocal sum is still performed in 3D, but a force and
941 potential correction applied in the ``z`` dimension to produce a
942 pseudo-2D summation. If your system has a slab geometry in the
943 ``x-y`` plane you can try to increase the ``z``-dimension of the box
944 (a box height of 3 times the slab height is usually ok) and use
947 .. mdp:: epsilon-surface
950 This controls the dipole correction to the Ewald summation in
951 3D. The default value of zero means it is turned off. Turn it on by
952 setting it to the value of the relative permittivity of the
953 imaginary surface around your infinite system. Be careful - you
954 shouldn't use this if you have free mobile charges in your
955 system. This value does not affect the slab 3DC variant of the long
966 No temperature coupling.
968 .. mdp-value:: berendsen
970 Temperature coupling with a Berendsen thermostat to a bath with
971 temperature :mdp:`ref-t`, with time constant
972 :mdp:`tau-t`. Several groups can be coupled separately, these
973 are specified in the :mdp:`tc-grps` field separated by spaces.
975 .. mdp-value:: nose-hoover
977 Temperature coupling using a Nose-Hoover extended ensemble. The
978 reference temperature and coupling groups are selected as above,
979 but in this case :mdp:`tau-t` controls the period of the
980 temperature fluctuations at equilibrium, which is slightly
981 different from a relaxation time. For NVT simulations the
982 conserved energy quantity is written to the energy and log files.
984 .. mdp-value:: andersen
986 Temperature coupling by randomizing a fraction of the particle velocities
987 at each timestep. Reference temperature and coupling groups are
988 selected as above. :mdp:`tau-t` is the average time between
989 randomization of each molecule. Inhibits particle dynamics
990 somewhat, but little or no ergodicity issues. Currently only
991 implemented with velocity Verlet, and not implemented with
994 .. mdp-value:: andersen-massive
996 Temperature coupling by randomizing velocities of all particles at
997 infrequent timesteps. Reference temperature and coupling groups are
998 selected as above. :mdp:`tau-t` is the time between
999 randomization of all molecules. Inhibits particle dynamics
1000 somewhat, but little or no ergodicity issues. Currently only
1001 implemented with velocity Verlet.
1003 .. mdp-value:: v-rescale
1005 Temperature coupling using velocity rescaling with a stochastic
1006 term (JCP 126, 014101). This thermostat is similar to Berendsen
1007 coupling, with the same scaling using :mdp:`tau-t`, but the
1008 stochastic term ensures that a proper canonical ensemble is
1009 generated. The random seed is set with :mdp:`ld-seed`. This
1010 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1011 simulations the conserved energy quantity is written to the
1012 energy and log file.
1017 The frequency for coupling the temperature. The default value of -1
1018 sets :mdp:`nsttcouple` equal to 10, or fewer steps if required
1019 for accurate integration. Note that the default value is not 1
1020 because additional computation and communication is required for
1021 obtaining the kinetic energy. For velocity
1022 Verlet integrators :mdp:`nsttcouple` is set to 1.
1024 .. mdp:: nh-chain-length
1027 The number of chained Nose-Hoover thermostats for velocity Verlet
1028 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1029 only supports 1. Data for the NH chain variables is not printed
1030 to the :ref:`edr` file by default, but can be turned on with the
1031 :mdp:`print-nose-hoover-chain-variables` option.
1033 .. mdp:: print-nose-hoover-chain-variables
1037 Do not store Nose-Hoover chain variables in the energy file.
1041 Store all positions and velocities of the Nose-Hoover chain
1046 groups to couple to separate temperature baths
1051 time constant for coupling (one for each group in
1052 :mdp:`tc-grps`), -1 means no temperature coupling
1057 reference temperature for coupling (one for each group in
1068 No pressure coupling. This means a fixed box size.
1070 .. mdp-value:: Berendsen
1072 Exponential relaxation pressure coupling with time constant
1073 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1074 argued that this does not yield a correct thermodynamic
1075 ensemble, but it is the most efficient way to scale a box at the
1078 .. mdp-value:: C-rescale
1080 Exponential relaxation pressure coupling with time constant
1081 :mdp:`tau-p`, including a stochastic term to enforce correct
1082 volume fluctuations. The box is scaled every :mdp:`nstpcouple`
1083 steps. It can be used for both equilibration and production.
1085 .. mdp-value:: Parrinello-Rahman
1087 Extended-ensemble pressure coupling where the box vectors are
1088 subject to an equation of motion. The equation of motion for the
1089 atoms is coupled to this. No instantaneous scaling takes
1090 place. As for Nose-Hoover temperature coupling the time constant
1091 :mdp:`tau-p` is the period of pressure fluctuations at
1092 equilibrium. This is probably a better method when you want to
1093 apply pressure scaling during data collection, but beware that
1094 you can get very large oscillations if you are starting from a
1095 different pressure. For simulations where the exact fluctations
1096 of the NPT ensemble are important, or if the pressure coupling
1097 time is very short it may not be appropriate, as the previous
1098 time step pressure is used in some steps of the |Gromacs|
1099 implementation for the current time step pressure.
1103 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1104 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1105 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1106 time constant :mdp:`tau-p` is the period of pressure
1107 fluctuations at equilibrium. This is probably a better method
1108 when you want to apply pressure scaling during data collection,
1109 but beware that you can get very large oscillations if you are
1110 starting from a different pressure. Currently (as of version
1111 5.1), it only supports isotropic scaling, and only works without
1116 Specifies the kind of isotropy of the pressure coupling used. Each
1117 kind takes one or more values for :mdp:`compressibility` and
1118 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1120 .. mdp-value:: isotropic
1122 Isotropic pressure coupling with time constant
1123 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1124 :mdp:`ref-p` is required.
1126 .. mdp-value:: semiisotropic
1128 Pressure coupling which is isotropic in the ``x`` and ``y``
1129 direction, but different in the ``z`` direction. This can be
1130 useful for membrane simulations. Two values each for
1131 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1132 ``x/y`` and ``z`` directions respectively.
1134 .. mdp-value:: anisotropic
1136 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1137 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1138 respectively. When the off-diagonal compressibilities are set to
1139 zero, a rectangular box will stay rectangular. Beware that
1140 anisotropic scaling can lead to extreme deformation of the
1143 .. mdp-value:: surface-tension
1145 Surface tension coupling for surfaces parallel to the
1146 xy-plane. Uses normal pressure coupling for the ``z``-direction,
1147 while the surface tension is coupled to the ``x/y`` dimensions of
1148 the box. The first :mdp:`ref-p` value is the reference surface
1149 tension times the number of surfaces ``bar nm``, the second
1150 value is the reference ``z``-pressure ``bar``. The two
1151 :mdp:`compressibility` values are the compressibility in the
1152 ``x/y`` and ``z`` direction respectively. The value for the
1153 ``z``-compressibility should be reasonably accurate since it
1154 influences the convergence of the surface-tension, it can also
1155 be set to zero to have a box with constant height.
1160 The frequency for coupling the pressure. The default value of -1
1161 sets :mdp:`nstpcouple` equal to 10, or fewer steps if required
1162 for accurate integration. Note that the default value is not 1
1163 because additional computation and communication is required for
1164 obtaining the virial. For velocity
1165 Verlet integrators :mdp:`nstpcouple` is set to 1.
1170 The time constant for pressure coupling (one value for all
1173 .. mdp:: compressibility
1176 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1177 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1178 required values is implied by :mdp:`pcoupltype`.
1183 The reference pressure for coupling. The number of required values
1184 is implied by :mdp:`pcoupltype`.
1186 .. mdp:: refcoord-scaling
1190 The reference coordinates for position restraints are not
1191 modified. Note that with this option the virial and pressure
1192 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1197 The reference coordinates are scaled with the scaling matrix of
1198 the pressure coupling.
1202 Scale the center of mass of the reference coordinates with the
1203 scaling matrix of the pressure coupling. The vectors of each
1204 reference coordinate to the center of mass are not scaled. Only
1205 one COM is used, even when there are multiple molecules with
1206 position restraints. For calculating the COM of the reference
1207 coordinates in the starting configuration, periodic boundary
1208 conditions are not taken into account. Note that with this option
1209 the virial and pressure might be ill defined, see
1210 :ref:`here <reference-manual-position-restraints>` for more details.
1216 Simulated annealing is controlled separately for each temperature
1217 group in |Gromacs|. The reference temperature is a piecewise linear
1218 function, but you can use an arbitrary number of points for each
1219 group, and choose either a single sequence or a periodic behaviour for
1220 each group. The actual annealing is performed by dynamically changing
1221 the reference temperature used in the thermostat algorithm selected,
1222 so remember that the system will usually not instantaneously reach the
1223 reference temperature!
1227 Type of annealing for each temperature group
1231 No simulated annealing - just couple to reference temperature value.
1233 .. mdp-value:: single
1235 A single sequence of annealing points. If your simulation is
1236 longer than the time of the last point, the temperature will be
1237 coupled to this constant value after the annealing sequence has
1238 reached the last time point.
1240 .. mdp-value:: periodic
1242 The annealing will start over at the first reference point once
1243 the last reference time is reached. This is repeated until the
1246 .. mdp:: annealing-npoints
1248 A list with the number of annealing reference/control points used
1249 for each temperature group. Use 0 for groups that are not
1250 annealed. The number of entries should equal the number of
1253 .. mdp:: annealing-time
1255 List of times at the annealing reference/control points for each
1256 group. If you are using periodic annealing, the times will be used
1257 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1258 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1259 etc. The number of entries should equal the sum of the numbers
1260 given in :mdp:`annealing-npoints`.
1262 .. mdp:: annealing-temp
1264 List of temperatures at the annealing reference/control points for
1265 each group. The number of entries should equal the sum of the
1266 numbers given in :mdp:`annealing-npoints`.
1268 Confused? OK, let's use an example. Assume you have two temperature
1269 groups, set the group selections to ``annealing = single periodic``,
1270 the number of points of each group to ``annealing-npoints = 3 4``, the
1271 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1272 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1273 will be coupled to 298K at 0ps, but the reference temperature will
1274 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1275 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1276 second group is coupled to 298K at 0ps, it increases linearly to 320K
1277 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1278 decreases to 298K, and then it starts over with the same pattern
1279 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1280 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1290 Do not generate velocities. The velocities are set to zero
1291 when there are no velocities in the input structure file.
1295 Generate velocities in :ref:`gmx grompp` according to a
1296 Maxwell distribution at temperature :mdp:`gen-temp`, with
1297 random seed :mdp:`gen-seed`. This is only meaningful with
1298 :mdp-value:`integrator=md`.
1303 temperature for Maxwell distribution
1308 used to initialize random generator for random velocities,
1309 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1316 .. mdp:: constraints
1318 Controls which bonds in the topology will be converted to rigid
1319 holonomic constraints. Note that typical rigid water models do not
1320 have bonds, but rather a specialized ``[settles]`` directive, so
1321 are not affected by this keyword.
1325 No bonds converted to constraints.
1327 .. mdp-value:: h-bonds
1329 Convert the bonds with H-atoms to constraints.
1331 .. mdp-value:: all-bonds
1333 Convert all bonds to constraints.
1335 .. mdp-value:: h-angles
1337 Convert all bonds to constraints and convert the angles that
1338 involve H-atoms to bond-constraints.
1340 .. mdp-value:: all-angles
1342 Convert all bonds to constraints and all angles to bond-constraints.
1344 .. mdp:: constraint-algorithm
1346 Chooses which solver satisfies any non-SETTLE holonomic
1349 .. mdp-value:: LINCS
1351 LINear Constraint Solver. With domain decomposition the parallel
1352 version P-LINCS is used. The accuracy in set with
1353 :mdp:`lincs-order`, which sets the number of matrices in the
1354 expansion for the matrix inversion. After the matrix inversion
1355 correction the algorithm does an iterative correction to
1356 compensate for lengthening due to rotation. The number of such
1357 iterations can be controlled with :mdp:`lincs-iter`. The root
1358 mean square relative constraint deviation is printed to the log
1359 file every :mdp:`nstlog` steps. If a bond rotates more than
1360 :mdp:`lincs-warnangle` in one step, a warning will be printed
1361 both to the log file and to ``stderr``. LINCS should not be used
1362 with coupled angle constraints.
1364 .. mdp-value:: SHAKE
1366 SHAKE is slightly slower and less stable than LINCS, but does
1367 work with angle constraints. The relative tolerance is set with
1368 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1369 does not support constraints between atoms on different
1370 decomposition domains, so it can only be used with domain
1371 decomposition when so-called update-groups are used, which is
1372 usally the case when only bonds involving hydrogens are
1373 constrained. SHAKE can not be used with energy minimization.
1375 .. mdp:: continuation
1377 This option was formerly known as ``unconstrained-start``.
1381 apply constraints to the start configuration and reset shells
1385 do not apply constraints to the start configuration and do not
1386 reset shells, useful for exact coninuation and reruns
1391 relative tolerance for SHAKE
1393 .. mdp:: lincs-order
1396 Highest order in the expansion of the constraint coupling
1397 matrix. When constraints form triangles, an additional expansion of
1398 the same order is applied on top of the normal expansion only for
1399 the couplings within such triangles. For "normal" MD simulations an
1400 order of 4 usually suffices, 6 is needed for large time-steps with
1401 virtual sites or BD. For accurate energy minimization an order of 8
1402 or more might be required. With domain decomposition, the cell size
1403 is limited by the distance spanned by :mdp:`lincs-order` +1
1404 constraints. When one wants to scale further than this limit, one
1405 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1406 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1407 )* :mdp:`lincs-order` remains constant.
1412 Number of iterations to correct for rotational lengthening in
1413 LINCS. For normal runs a single step is sufficient, but for NVE
1414 runs where you want to conserve energy accurately or for accurate
1415 energy minimization you might want to increase it to 2.
1417 .. mdp:: lincs-warnangle
1420 maximum angle that a bond can rotate before LINCS will complain
1426 bonds are represented by a harmonic potential
1430 bonds are represented by a Morse potential
1433 Energy group exclusions
1434 ^^^^^^^^^^^^^^^^^^^^^^^
1436 .. mdp:: energygrp-excl
1438 Pairs of energy groups for which all non-bonded interactions are
1439 excluded. An example: if you have two energy groups ``Protein`` and
1440 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1441 would give only the non-bonded interactions between the protein and
1442 the solvent. This is especially useful for speeding up energy
1443 calculations with ``mdrun -rerun`` and for excluding interactions
1444 within frozen groups.
1453 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1454 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1455 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1456 used (it is usually best to use semiisotropic pressure coupling
1457 with the ``x/y`` compressibility set to 0, as otherwise the surface
1458 area will change). Walls interact wit the rest of the system
1459 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1460 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1461 monitor the interaction of energy groups with each wall. The center
1462 of mass motion removal will be turned off in the ``z``-direction.
1464 .. mdp:: wall-atomtype
1466 the atom type name in the force field for each wall. By (for
1467 example) defining a special wall atom type in the topology with its
1468 own combination rules, this allows for independent tuning of the
1469 interaction of each atomtype with the walls.
1475 LJ integrated over the volume behind the wall: 9-3 potential
1479 LJ integrated over the wall surface: 10-4 potential
1483 direct LJ potential with the ``z`` distance from the wall
1487 user defined potentials indexed with the ``z`` distance from the
1488 wall, the tables are read analogously to the
1489 :mdp:`energygrp-table` option, where the first name is for a
1490 "normal" energy group and the second name is ``wall0`` or
1491 ``wall1``, only the dispersion and repulsion columns are used
1493 .. mdp:: wall-r-linpot
1496 Below this distance from the wall the potential is continued
1497 linearly and thus the force is constant. Setting this option to a
1498 postive value is especially useful for equilibration when some
1499 atoms are beyond a wall. When the value is <=0 (<0 for
1500 :mdp:`wall-type` =table), a fatal error is generated when atoms
1503 .. mdp:: wall-density
1505 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1506 the number density of the atoms for each wall for wall types 9-3
1509 .. mdp:: wall-ewald-zfac
1512 The scaling factor for the third box vector for Ewald summation
1513 only, the minimum is 2. Ewald summation can only be used with
1514 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1515 ``=3dc``. The empty layer in the box serves to decrease the
1516 unphysical Coulomb interaction between periodic images.
1522 Note that where pulling coordinates are applicable, there can be more
1523 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1524 variables will exist accordingly. Documentation references to things
1525 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1526 applicable pulling coordinate, eg. the second pull coordinate is described by
1527 pull-coord2-vec, pull-coord2-k, and so on.
1533 No center of mass pulling. All the following pull options will
1534 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1539 Center of mass pulling will be applied on 1 or more groups using
1540 1 or more pull coordinates.
1542 .. mdp:: pull-cylinder-r
1545 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1547 .. mdp:: pull-constr-tol
1550 the relative constraint tolerance for constraint pulling
1552 .. mdp:: pull-print-com
1556 do not print the COM for any group
1560 print the COM of all groups for all pull coordinates
1562 .. mdp:: pull-print-ref-value
1566 do not print the reference value for each pull coordinate
1570 print the reference value for each pull coordinate
1572 .. mdp:: pull-print-components
1576 only print the distance for each pull coordinate
1580 print the distance and Cartesian components selected in
1581 :mdp:`pull-coord1-dim`
1583 .. mdp:: pull-nstxout
1586 frequency for writing out the COMs of all the pull group (0 is
1589 .. mdp:: pull-nstfout
1592 frequency for writing out the force of all the pulled group
1595 .. mdp:: pull-pbc-ref-prev-step-com
1599 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1600 treatment of periodic boundary conditions.
1604 Use the COM of the previous step as reference for the treatment
1605 of periodic boundary conditions. The reference is initialized
1606 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1607 be located centrally in the group. Using the COM from the
1608 previous step can be useful if one or more pull groups are large.
1610 .. mdp:: pull-xout-average
1614 Write the instantaneous coordinates for all the pulled groups.
1618 Write the average coordinates (since last output) for all the
1619 pulled groups. N.b., some analysis tools might expect instantaneous
1622 .. mdp:: pull-fout-average
1626 Write the instantaneous force for all the pulled groups.
1630 Write the average force (since last output) for all the
1631 pulled groups. N.b., some analysis tools might expect instantaneous
1634 .. mdp:: pull-ngroups
1637 The number of pull groups, not including the absolute reference
1638 group, when used. Pull groups can be reused in multiple pull
1639 coordinates. Below only the pull options for group 1 are given,
1640 further groups simply increase the group index number.
1642 .. mdp:: pull-ncoords
1645 The number of pull coordinates. Below only the pull options for
1646 coordinate 1 are given, further coordinates simply increase the
1647 coordinate index number.
1649 .. mdp:: pull-group1-name
1651 The name of the pull group, is looked up in the index file or in
1652 the default groups to obtain the atoms involved.
1654 .. mdp:: pull-group1-weights
1656 Optional relative weights which are multiplied with the masses of
1657 the atoms to give the total weight for the COM. The number should
1658 be 0, meaning all 1, or the number of atoms in the pull group.
1660 .. mdp:: pull-group1-pbcatom
1663 The reference atom for the treatment of periodic boundary
1664 conditions inside the group (this has no effect on the treatment of
1665 the pbc between groups). This option is only important when the
1666 diameter of the pull group is larger than half the shortest box
1667 vector. For determining the COM, all atoms in the group are put at
1668 their periodic image which is closest to
1669 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1670 atom (number wise) is used, which is only safe for small groups.
1671 :ref:`gmx grompp` checks that the maximum distance from the reference
1672 atom (specifically chosen, or not) to the other atoms in the group
1673 is not too large. This parameter is not used with
1674 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1675 weighting, which is useful for a group of molecules in a periodic
1676 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1679 .. mdp:: pull-coord1-type
1681 .. mdp-value:: umbrella
1683 Center of mass pulling using an umbrella potential between the
1684 reference group and one or more groups.
1686 .. mdp-value:: constraint
1688 Center of mass pulling using a constraint between the reference
1689 group and one or more groups. The setup is identical to the
1690 option umbrella, except for the fact that a rigid constraint is
1691 applied instead of a harmonic potential. Note that this type is
1692 not supported in combination with multiple time stepping.
1694 .. mdp-value:: constant-force
1696 Center of mass pulling using a linear potential and therefore a
1697 constant force. For this option there is no reference position
1698 and therefore the parameters :mdp:`pull-coord1-init` and
1699 :mdp:`pull-coord1-rate` are not used.
1701 .. mdp-value:: flat-bottom
1703 At distances above :mdp:`pull-coord1-init` a harmonic potential
1704 is applied, otherwise no potential is applied.
1706 .. mdp-value:: flat-bottom-high
1708 At distances below :mdp:`pull-coord1-init` a harmonic potential
1709 is applied, otherwise no potential is applied.
1711 .. mdp-value:: external-potential
1713 An external potential that needs to be provided by another
1716 .. mdp:: pull-coord1-potential-provider
1718 The name of the external module that provides the potential for
1719 the case where :mdp:`pull-coord1-type` is external-potential.
1721 .. mdp:: pull-coord1-geometry
1723 .. mdp-value:: distance
1725 Pull along the vector connecting the two groups. Components can
1726 be selected with :mdp:`pull-coord1-dim`.
1728 .. mdp-value:: direction
1730 Pull in the direction of :mdp:`pull-coord1-vec`.
1732 .. mdp-value:: direction-periodic
1734 As :mdp-value:`pull-coord1-geometry=direction`, but does not apply
1735 periodic box vector corrections to keep the distance within half
1736 the box length. This is (only) useful for pushing groups apart
1737 by more than half the box length by continuously changing the reference
1738 location using a pull rate. With this geometry the box should not be
1739 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1740 the pull force is not added to the virial.
1742 .. mdp-value:: direction-relative
1744 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1745 that points from the COM of a third to the COM of a fourth pull
1746 group. This means that 4 groups need to be supplied in
1747 :mdp:`pull-coord1-groups`. Note that the pull force will give
1748 rise to a torque on the pull vector, which is turn leads to
1749 forces perpendicular to the pull vector on the two groups
1750 defining the vector. If you want a pull group to move between
1751 the two groups defining the vector, simply use the union of
1752 these two groups as the reference group.
1754 .. mdp-value:: cylinder
1756 Designed for pulling with respect to a layer where the reference
1757 COM is given by a local cylindrical part of the reference group.
1758 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1759 the first of the two groups in :mdp:`pull-coord1-groups` a
1760 cylinder is selected around the axis going through the COM of
1761 the second group with direction :mdp:`pull-coord1-vec` with
1762 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1763 continously to zero as the radial distance goes from 0 to
1764 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1765 dependence gives rise to radial forces on both pull groups.
1766 Note that the radius should be smaller than half the box size.
1767 For tilted cylinders they should be even smaller than half the
1768 box size since the distance of an atom in the reference group
1769 from the COM of the pull group has both a radial and an axial
1770 component. This geometry is not supported with constraint
1773 .. mdp-value:: angle
1775 Pull along an angle defined by four groups. The angle is
1776 defined as the angle between two vectors: the vector connecting
1777 the COM of the first group to the COM of the second group and
1778 the vector connecting the COM of the third group to the COM of
1781 .. mdp-value:: angle-axis
1783 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1784 Thus, only the two groups that define the first vector need to be given.
1786 .. mdp-value:: dihedral
1788 Pull along a dihedral angle defined by six groups. These pairwise
1789 define three vectors: the vector connecting the COM of group 1
1790 to the COM of group 2, the COM of group 3 to the COM of group 4,
1791 and the COM of group 5 to the COM group 6. The dihedral angle is
1792 then defined as the angle between two planes: the plane spanned by the
1793 the two first vectors and the plane spanned the two last vectors.
1795 .. mdp-value:: transformation
1797 Transforms other pull coordinates using a mathematical expression defined by :mdp:`pull-coord1-expression`.
1798 Pull coordinates of lower indices can be used as variables to this pull coordinate.
1799 Thus, pull transformation coordinates should have a higher pull coordinate index
1800 than all pull coordinates they transform.
1802 .. mdp:: pull-coord1-expression
1804 Mathematical expression to transform pull coordinates of lower indices to a new one.
1805 The pull coordinates are referred to as variables in the equation so that
1806 pull-coord1's value becomes 'x1', pull-coord2 value becomes 'x2' etc.
1807 The mathematical expression are evaluated using muParser.
1808 Only relevant if :mdp:`pull-coord1-geometry` is set to :mdp-value:`transformation`.
1810 .. mdp:: pull-coord1-dx
1813 Size of finite difference to use in numerical derivation of the pull coordinate
1814 with respect to other pull coordinates.
1815 The current implementation uses a simple first order finite difference method to perform derivation so that
1816 f'(x) = (f(x+dx)-f(x))/dx
1817 Only relevant if :mdp:`pull-coord1-geometry` is set to :mdp-value:`transformation`.
1819 .. mdp:: pull-coord1-groups
1821 The group indices on which this pull coordinate will operate.
1822 The number of group indices required is geometry dependent.
1823 The first index can be 0, in which case an
1824 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1825 absolute reference the system is no longer translation invariant
1826 and one should think about what to do with the center of mass
1829 .. mdp:: pull-coord1-dim
1832 Selects the dimensions that this pull coordinate acts on and that
1833 are printed to the output files when
1834 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1835 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1836 components set to Y contribute to the distance. Thus setting this
1837 to Y Y N results in a distance in the x/y plane. With other
1838 geometries all dimensions with non-zero entries in
1839 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1840 dimensions only affect the output.
1842 .. mdp:: pull-coord1-origin
1845 The pull reference position for use with an absolute reference.
1847 .. mdp:: pull-coord1-vec
1850 The pull direction. :ref:`gmx grompp` normalizes the vector.
1852 .. mdp:: pull-coord1-start
1856 do not modify :mdp:`pull-coord1-init`
1860 add the COM distance of the starting conformation to
1861 :mdp:`pull-coord1-init`
1863 .. mdp:: pull-coord1-init
1866 The reference distance or reference angle at t=0.
1868 .. mdp:: pull-coord1-rate
1870 (0) [nm/ps] or [deg/ps]
1871 The rate of change of the reference position or reference angle.
1873 .. mdp:: pull-coord1-k
1875 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1876 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1877 The force constant. For umbrella pulling this is the harmonic force
1878 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1879 for angles). For constant force pulling this is the
1880 force constant of the linear potential, and thus the negative (!)
1881 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1882 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1883 Note that for angles the force constant is expressed in terms of radians
1884 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1886 .. mdp:: pull-coord1-kB
1888 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1889 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1890 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1891 :mdp:`free-energy` is turned on. The force constant is then (1 -
1892 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1894 AWH adaptive biasing
1895 ^^^^^^^^^^^^^^^^^^^^
1905 Adaptively bias a reaction coordinate using the AWH method and estimate
1906 the corresponding PMF. The PMF and other AWH data are written to energy
1907 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1908 the ``gmx awh`` tool. The AWH coordinate can be
1909 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1910 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1911 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1912 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1914 .. mdp:: awh-potential
1916 .. mdp-value:: convolved
1918 The applied biasing potential is the convolution of the bias function and a
1919 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1920 in a smooth potential function and force. The resolution of the potential is set
1921 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`. This option is not
1922 compatible with using the free energy lambda state as an AWH reaction coordinate.
1924 .. mdp-value:: umbrella
1926 The potential bias is applied by controlling the position of an harmonic potential
1927 using Monte-Carlo sampling. The force constant is set with
1928 :mdp:`awh1-dim1-force-constant`. The umbrella location
1929 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1930 This is option is required when using the free energy lambda state as an AWH reaction coordinate.
1931 Apart from that, this option is mainly for comparison
1932 and testing purposes as there are no advantages to using an umbrella.
1934 .. mdp:: awh-share-multisim
1938 AWH will not share biases across simulations started with
1939 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1943 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1944 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1945 with the biases with the same :mdp:`awh1-share-group` value.
1946 The simulations should have the same AWH settings for sharing to make sense.
1947 :ref:`gmx mdrun` will check whether the simulations are technically
1948 compatible for sharing, but the user should check that bias sharing
1949 physically makes sense.
1953 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1954 where -1 indicates to generate a seed. Only used with
1955 :mdp-value:`awh-potential=umbrella`.
1960 Number of steps between printing AWH data to the energy file, should be
1961 a multiple of :mdp:`nstenergy`.
1963 .. mdp:: awh-nstsample
1966 Number of steps between sampling of the coordinate value. This sampling
1967 is the basis for updating the bias and estimating the PMF and other AWH observables.
1969 .. mdp:: awh-nsamples-update
1972 The number of coordinate samples used for each AWH update.
1973 The update interval in steps is :mdp:`awh-nstsample` times this value.
1978 The number of biases, each acting on its own coordinate.
1979 The following options should be specified
1980 for each bias although below only the options for bias number 1 is shown. Options for
1981 other bias indices are obtained by replacing '1' by the bias index.
1983 .. mdp:: awh1-error-init
1985 (10.0) [kJ mol\ :sup:`-1`]
1986 Estimated initial average error of the PMF for this bias. This value together with the
1987 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1988 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1990 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1991 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1992 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1993 then :mdp:`awh1-error-init` should reflect that knowledge.
1995 .. mdp:: awh1-growth
1997 .. mdp-value:: exp-linear
1999 Each bias keeps a reference weight histogram for the coordinate samples.
2000 Its size sets the magnitude of the bias function and free energy estimate updates
2001 (few samples corresponds to large updates and vice versa).
2002 Thus, its growth rate sets the maximum convergence rate.
2003 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
2004 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
2005 The initial stage is typically necessary for efficient convergence when starting a new simulation where
2006 high free energy barriers have not yet been flattened by the bias.
2008 .. mdp-value:: linear
2010 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
2011 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
2012 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
2014 .. mdp:: awh1-equilibrate-histogram
2018 Do not equilibrate histogram.
2022 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
2023 histogram of sampled weights is following the target distribution closely enough (specifically,
2024 at least 80% of the target region needs to have a local relative error of less than 20%). This
2025 option would typically only be used when :mdp:`awh1-share-group` > 0
2026 and the initial configurations poorly represent the target
2029 .. mdp:: awh1-target
2031 .. mdp-value:: constant
2033 The bias is tuned towards a constant (uniform) coordinate distribution
2034 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
2036 .. mdp-value:: cutoff
2038 Similar to :mdp-value:`awh1-target=constant`, but the target
2039 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
2040 where F is the free energy relative to the estimated global minimum.
2041 This provides a smooth switch of a flat target distribution in
2042 regions with free energy lower than the cut-off to a Boltzmann
2043 distribution in regions with free energy higher than the cut-off.
2045 .. mdp-value:: boltzmann
2047 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
2048 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
2049 would give the same coordinate distribution as sampling with a simulation temperature
2052 .. mdp-value:: local-boltzmann
2054 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
2055 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
2056 change of the bias only depends on the local sampling. This local convergence property is
2057 only compatible with :mdp-value:`awh1-growth=linear`, since for
2058 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
2060 .. mdp:: awh1-target-beta-scaling
2063 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
2064 it is the unitless beta scaling factor taking values in (0,1).
2066 .. mdp:: awh1-target-cutoff
2068 (0) [kJ mol\ :sup:`-1`]
2069 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2071 .. mdp:: awh1-user-data
2075 Initialize the PMF and target distribution with default values.
2079 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2080 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2081 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2082 The file name can be changed with the ``-awh`` option.
2083 The first :mdp:`awh1-ndim` columns of
2084 each input file should contain the coordinate values, such that each row defines a point in
2085 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value (in kT) for each point.
2086 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2087 be in the same column as written by :ref:`gmx awh`.
2089 .. mdp:: awh1-share-group
2093 Do not share the bias.
2095 .. mdp-value:: positive
2097 Share the bias and PMF estimates within and/or between simulations.
2098 Within a simulation, the bias will be shared between biases that have the
2099 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2100 With :mdp-value:`awh-share-multisim=yes` and
2101 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2102 Sharing may increase convergence initially, although the starting configurations
2103 can be critical, especially when sharing between many biases.
2104 Currently, positive group values should start at 1 and increase
2105 by 1 for each subsequent bias that is shared.
2110 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2111 The following options should be specified for each such dimension. Below only
2112 the options for dimension number 1 is shown. Options for other dimension indices are
2113 obtained by replacing '1' by the dimension index.
2115 .. mdp:: awh1-dim1-coord-provider
2119 The pull module is providing the reaction coordinate for this dimension.
2120 With multiple time-stepping, AWH and pull should be in the same MTS level.
2122 .. mdp-value:: fep-lambda
2124 The free energy lambda state is the reaction coordinate for this dimension.
2125 The lambda states to use are specified by :mdp:`fep-lambdas`, :mdp:`vdw-lambdas`,
2126 :mdp:`coul-lambdas` etc. This is not compatible with delta-lambda. It also requires
2127 calc-lambda-neighbors to be -1. With multiple time-stepping, AWH should
2128 be in the slow level. This option requires :mdp-value:`awh-potential=umbrella`.
2130 .. mdp:: awh1-dim1-coord-index
2133 Index of the pull coordinate defining this coordinate dimension.
2135 .. mdp:: awh1-dim1-force-constant
2137 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2138 Force constant for the (convolved) umbrella potential(s) along this
2139 coordinate dimension.
2141 .. mdp:: awh1-dim1-start
2144 Start value of the sampling interval along this dimension. The range of allowed
2145 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2146 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2147 is allowed. The interval will then wrap around from +period/2 to -period/2.
2148 For the direction geometry, the dimension is made periodic when
2149 the direction is along a box vector and covers more than 95%
2150 of the box length. Note that one should not apply pressure coupling
2151 along a periodic dimension.
2153 .. mdp:: awh1-dim1-end
2156 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2158 .. mdp:: awh1-dim1-diffusion
2160 (10\ :sup:`-5`) [nm\ :sup:`2`/ps], [rad\ :sup:`2`/ps] or [ps\ :sup:`-1`]
2161 Estimated diffusion constant for this coordinate dimension determining the initial
2162 biasing rate. This needs only be a rough estimate and should not critically
2163 affect the results unless it is set to something very low, leading to slow convergence,
2164 or very high, forcing the system far from equilibrium. Not setting this value
2165 explicitly generates a warning.
2167 .. mdp:: awh1-dim1-cover-diameter
2170 Diameter that needs to be sampled by a single simulation around a coordinate value
2171 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2172 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2173 across each coordinate value.
2174 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2175 (:mdp:`awh1-share-group`>0).
2176 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2177 for many sharing simulations does not guarantee transitions across free energy barriers.
2178 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2179 has independently sampled the whole interval.
2184 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2185 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2186 that can be used to achieve such a rotation.
2192 No enforced rotation will be applied. All enforced rotation options will
2193 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2198 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2199 under the :mdp:`rot-group0` option.
2201 .. mdp:: rot-ngroups
2204 Number of rotation groups.
2208 Name of rotation group 0 in the index file.
2213 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2214 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2215 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2220 Use mass weighted rotation group positions.
2225 Rotation vector, will get normalized.
2230 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2234 (0) [degree ps\ :sup:`-1`]
2235 Reference rotation rate of group 0.
2239 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2240 Force constant for group 0.
2242 .. mdp:: rot-slab-dist0
2245 Slab distance, if a flexible axis rotation type was chosen.
2247 .. mdp:: rot-min-gauss0
2250 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2251 (for the flexible axis potentials).
2255 (0.0001) [nm\ :sup:`2`]
2256 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2258 .. mdp:: rot-fit-method0
2261 Fitting method when determining the actual angle of a rotation group
2262 (can be one of ``rmsd``, ``norm``, or ``potential``).
2264 .. mdp:: rot-potfit-nsteps0
2267 For fit type ``potential``, the number of angular positions around the reference angle for which the
2268 rotation potential is evaluated.
2270 .. mdp:: rot-potfit-step0
2273 For fit type ``potential``, the distance in degrees between two angular positions.
2275 .. mdp:: rot-nstrout
2278 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2279 and the rotation potential energy.
2281 .. mdp:: rot-nstsout
2284 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2294 ignore distance restraint information in topology file
2296 .. mdp-value:: simple
2298 simple (per-molecule) distance restraints.
2300 .. mdp-value:: ensemble
2302 distance restraints over an ensemble of molecules in one
2303 simulation box. Normally, one would perform ensemble averaging
2304 over multiple simulations, using ``mdrun
2305 -multidir``. The environment
2306 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2307 within each ensemble (usually equal to the number of directories
2308 supplied to ``mdrun -multidir``).
2310 .. mdp:: disre-weighting
2312 .. mdp-value:: equal
2314 divide the restraint force equally over all atom pairs in the
2317 .. mdp-value:: conservative
2319 the forces are the derivative of the restraint potential, this
2320 results in an weighting of the atom pairs to the reciprocal
2321 seventh power of the displacement. The forces are conservative
2322 when :mdp:`disre-tau` is zero.
2324 .. mdp:: disre-mixed
2328 the violation used in the calculation of the restraint force is
2329 the time-averaged violation
2333 the violation used in the calculation of the restraint force is
2334 the square root of the product of the time-averaged violation
2335 and the instantaneous violation
2339 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2340 force constant for distance restraints, which is multiplied by a
2341 (possibly) different factor for each restraint given in the ``fac``
2342 column of the interaction in the topology file.
2347 time constant for distance restraints running average. A value of
2348 zero turns off time averaging.
2350 .. mdp:: nstdisreout
2353 period between steps when the running time-averaged and
2354 instantaneous distances of all atom pairs involved in restraints
2355 are written to the energy file (can make the energy file very
2362 ignore orientation restraint information in topology file
2366 use orientation restraints, ensemble averaging can be performed
2367 with ``mdrun -multidir``
2371 (0) [kJ mol\ :sup:`-1`]
2372 force constant for orientation restraints, which is multiplied by a
2373 (possibly) different weight factor for each restraint, can be set
2374 to zero to obtain the orientations from a free simulation
2379 time constant for orientation restraints running average. A value
2380 of zero turns off time averaging.
2382 .. mdp:: orire-fitgrp
2384 fit group for orientation restraining. This group of atoms is used
2385 to determine the rotation **R** of the system with respect to the
2386 reference orientation. The reference orientation is the starting
2387 conformation of the first subsystem. For a protein, backbone is a
2390 .. mdp:: nstorireout
2393 period between steps when the running time-averaged and
2394 instantaneous orientations for all restraints, and the molecular
2395 order tensor are written to the energy file (can make the energy
2399 Free energy calculations
2400 ^^^^^^^^^^^^^^^^^^^^^^^^
2402 .. mdp:: free-energy
2406 Only use topology A.
2410 Interpolate between topology A (lambda=0) to topology B
2411 (lambda=1) and write the derivative of the Hamiltonian with
2412 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2413 or the Hamiltonian differences with respect to other lambda
2414 values (as specified with foreign lambda) to the energy file
2415 and/or to ``dhdl.xvg``, where they can be processed by, for
2416 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2417 are interpolated linearly as described in the manual. When
2418 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2419 used for the LJ and Coulomb interactions.
2423 Turns on expanded ensemble simulation, where the alchemical state
2424 becomes a dynamic variable, allowing jumping between different
2425 Hamiltonians. See the expanded ensemble options for controlling how
2426 expanded ensemble simulations are performed. The different
2427 Hamiltonians used in expanded ensemble simulations are defined by
2428 the other free energy options.
2430 .. mdp:: init-lambda
2433 starting value for lambda (float). Generally, this should only be
2434 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2435 other cases, :mdp:`init-lambda-state` should be specified
2436 instead. Must be greater than or equal to 0.
2438 .. mdp:: delta-lambda
2441 increment per time step for lambda
2443 .. mdp:: init-lambda-state
2446 starting value for the lambda state (integer). Specifies which
2447 columm of the lambda vector (:mdp:`coul-lambdas`,
2448 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2449 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2450 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2451 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2452 the first column, and so on.
2454 .. mdp:: fep-lambdas
2457 Zero, one or more lambda values for which Delta H values will be
2458 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2459 steps. Values must be between 0 and 1. Free energy differences
2460 between different lambda values can then be determined with
2461 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2462 other -lambdas keywords because all components of the lambda vector
2463 that are not specified will use :mdp:`fep-lambdas` (including
2464 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2466 .. mdp:: coul-lambdas
2469 Zero, one or more lambda values for which Delta H values will be
2470 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2471 steps. Values must be between 0 and 1. Only the electrostatic
2472 interactions are controlled with this component of the lambda
2473 vector (and only if the lambda=0 and lambda=1 states have differing
2474 electrostatic interactions).
2476 .. mdp:: vdw-lambdas
2479 Zero, one or more lambda values for which Delta H values will be
2480 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2481 steps. Values must be between 0 and 1. Only the van der Waals
2482 interactions are controlled with this component of the lambda
2485 .. mdp:: bonded-lambdas
2488 Zero, one or more lambda values for which Delta H values will be
2489 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2490 steps. Values must be between 0 and 1. Only the bonded interactions
2491 are controlled with this component of the lambda vector.
2493 .. mdp:: restraint-lambdas
2496 Zero, one or more lambda values for which Delta H values will be
2497 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2498 steps. Values must be between 0 and 1. Only the restraint
2499 interactions: dihedral restraints, and the pull code restraints are
2500 controlled with this component of the lambda vector.
2502 .. mdp:: mass-lambdas
2505 Zero, one or more lambda values for which Delta H values will be
2506 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2507 steps. Values must be between 0 and 1. Only the particle masses are
2508 controlled with this component of the lambda vector.
2510 .. mdp:: temperature-lambdas
2513 Zero, one or more lambda values for which Delta H values will be
2514 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2515 steps. Values must be between 0 and 1. Only the temperatures
2516 controlled with this component of the lambda vector. Note that
2517 these lambdas should not be used for replica exchange, only for
2518 simulated tempering.
2520 .. mdp:: calc-lambda-neighbors
2523 Controls the number of lambda values for which Delta H values will
2524 be calculated and written out, if :mdp:`init-lambda-state` has
2525 been set. A positive value will limit the number of lambda points
2526 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2527 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2528 has a value of 2, energies for lambda points 3-7 will be calculated
2529 and writen out. A value of -1 means all lambda points will be
2530 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2531 1 is sufficient, while for MBAR -1 should be used.
2536 the soft-core alpha parameter, a value of 0 results in linear
2537 interpolation of the LJ and Coulomb interactions
2542 power 6 for the radial term in the soft-core equation.
2547 Whether to apply the soft-core free energy interaction
2548 transformation to the Columbic interaction of a molecule. Default
2549 is no, as it is generally more efficient to turn off the Coulomic
2550 interactions linearly before turning off the van der Waals
2551 interactions. Note that it is only taken into account when lambda
2552 states are used, not with :mdp:`couple-lambda0` /
2553 :mdp:`couple-lambda1`, and you can still turn off soft-core
2554 interactions by setting :mdp:`sc-alpha` to 0.
2559 the power for lambda in the soft-core function, only the values 1
2565 the soft-core sigma for particles which have a C6 or C12 parameter
2566 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2568 .. mdp:: couple-moltype
2570 Here one can supply a molecule type (as defined in the topology)
2571 for calculating solvation or coupling free energies. There is a
2572 special option ``system`` that couples all molecule types in the
2573 system. This can be useful for equilibrating a system starting from
2574 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2575 on. The Van der Waals interactions and/or charges in this molecule
2576 type can be turned on or off between lambda=0 and lambda=1,
2577 depending on the settings of :mdp:`couple-lambda0` and
2578 :mdp:`couple-lambda1`. If you want to decouple one of several
2579 copies of a molecule, you need to copy and rename the molecule
2580 definition in the topology.
2582 .. mdp:: couple-lambda0
2584 .. mdp-value:: vdw-q
2586 all interactions are on at lambda=0
2590 the charges are zero (no Coulomb interactions) at lambda=0
2594 the Van der Waals interactions are turned at lambda=0; soft-core
2595 interactions will be required to avoid singularities
2599 the Van der Waals interactions are turned off and the charges
2600 are zero at lambda=0; soft-core interactions will be required to
2601 avoid singularities.
2603 .. mdp:: couple-lambda1
2605 analogous to :mdp:`couple-lambda1`, but for lambda=1
2607 .. mdp:: couple-intramol
2611 All intra-molecular non-bonded interactions for moleculetype
2612 :mdp:`couple-moltype` are replaced by exclusions and explicit
2613 pair interactions. In this manner the decoupled state of the
2614 molecule corresponds to the proper vacuum state without
2615 periodicity effects.
2619 The intra-molecular Van der Waals and Coulomb interactions are
2620 also turned on/off. This can be useful for partitioning
2621 free-energies of relatively large molecules, where the
2622 intra-molecular non-bonded interactions might lead to
2623 kinetically trapped vacuum conformations. The 1-4 pair
2624 interactions are not turned off.
2629 the frequency for writing dH/dlambda and possibly Delta H to
2630 dhdl.xvg, 0 means no ouput, should be a multiple of
2631 :mdp:`nstcalcenergy`.
2633 .. mdp:: dhdl-derivatives
2637 If yes (the default), the derivatives of the Hamiltonian with
2638 respect to lambda at each :mdp:`nstdhdl` step are written
2639 out. These values are needed for interpolation of linear energy
2640 differences with :ref:`gmx bar` (although the same can also be
2641 achieved with the right foreign lambda setting, that may not be as
2642 flexible), or with thermodynamic integration
2644 .. mdp:: dhdl-print-energy
2648 Include either the total or the potential energy in the dhdl
2649 file. Options are 'no', 'potential', or 'total'. This information
2650 is needed for later free energy analysis if the states of interest
2651 are at different temperatures. If all states are at the same
2652 temperature, this information is not needed. 'potential' is useful
2653 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2654 file. When rerunning from an existing trajectory, the kinetic
2655 energy will often not be correct, and thus one must compute the
2656 residual free energy from the potential alone, with the kinetic
2657 energy component computed analytically.
2659 .. mdp:: separate-dhdl-file
2663 The free energy values that are calculated (as specified with
2664 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2665 written out to a separate file, with the default name
2666 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2671 The free energy values are written out to the energy output file
2672 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2673 steps), where they can be extracted with :ref:`gmx energy` or
2674 used directly with :ref:`gmx bar`.
2676 .. mdp:: dh-hist-size
2679 If nonzero, specifies the size of the histogram into which the
2680 Delta H values (specified with foreign lambda) and the derivative
2681 dH/dl values are binned, and written to ener.edr. This can be used
2682 to save disk space while calculating free energy differences. One
2683 histogram gets written for each foreign lambda and two for the
2684 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2685 histogram settings (too small size or too wide bins) can introduce
2686 errors. Do not use histograms unless you're certain you need it.
2688 .. mdp:: dh-hist-spacing
2691 Specifies the bin width of the histograms, in energy units. Used in
2692 conjunction with :mdp:`dh-hist-size`. This size limits the
2693 accuracy with which free energies can be calculated. Do not use
2694 histograms unless you're certain you need it.
2697 Expanded Ensemble calculations
2698 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2700 .. mdp:: nstexpanded
2702 The number of integration steps beween attempted moves changing the
2703 system Hamiltonian in expanded ensemble simulations. Must be a
2704 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2711 No Monte Carlo in state space is performed.
2713 .. mdp-value:: metropolis-transition
2715 Uses the Metropolis weights to update the expanded ensemble
2716 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2719 .. mdp-value:: barker-transition
2721 Uses the Barker transition critera to update the expanded
2722 ensemble weight of each state i, defined by exp(-beta_new
2723 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2725 .. mdp-value:: wang-landau
2727 Uses the Wang-Landau algorithm (in state space, not energy
2728 space) to update the expanded ensemble weights.
2730 .. mdp-value:: min-variance
2732 Uses the minimum variance updating method of Escobedo et al. to
2733 update the expanded ensemble weights. Weights will not be the
2734 free energies, but will rather emphasize states that need more
2735 sampling to give even uncertainty.
2737 .. mdp:: lmc-mc-move
2741 No Monte Carlo in state space is performed.
2743 .. mdp-value:: metropolis-transition
2745 Randomly chooses a new state up or down, then uses the
2746 Metropolis critera to decide whether to accept or reject:
2747 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2749 .. mdp-value:: barker-transition
2751 Randomly chooses a new state up or down, then uses the Barker
2752 transition critera to decide whether to accept or reject:
2753 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2755 .. mdp-value:: gibbs
2757 Uses the conditional weights of the state given the coordinate
2758 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2761 .. mdp-value:: metropolized-gibbs
2763 Uses the conditional weights of the state given the coordinate
2764 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2765 to move to, EXCLUDING the current state, then uses a rejection
2766 step to ensure detailed balance. Always more efficient that
2767 Gibbs, though only marginally so in many situations, such as
2768 when only the nearest neighbors have decent phase space
2774 random seed to use for Monte Carlo moves in state space. When
2775 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2777 .. mdp:: mc-temperature
2779 Temperature used for acceptance/rejection for Monte Carlo moves. If
2780 not specified, the temperature of the simulation specified in the
2781 first group of :mdp:`ref-t` is used.
2786 The cutoff for the histogram of state occupancies to be reset, and
2787 the free energy incrementor to be changed from delta to delta *
2788 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2789 each histogram) / (average number of samples at each
2790 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2791 histogram is only considered flat if all Nratio > 0.8 AND
2792 simultaneously all 1/Nratio > 0.8.
2797 Each time the histogram is considered flat, then the current value
2798 of the Wang-Landau incrementor for the free energies is multiplied
2799 by :mdp:`wl-scale`. Value must be between 0 and 1.
2801 .. mdp:: init-wl-delta
2804 The initial value of the Wang-Landau incrementor in kT. Some value
2805 near 1 kT is usually most efficient, though sometimes a value of
2806 2-3 in units of kT works better if the free energy differences are
2809 .. mdp:: wl-oneovert
2812 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2813 the large sample limit. There is significant evidence that the
2814 standard Wang-Landau algorithms in state space presented here
2815 result in free energies getting 'burned in' to incorrect values
2816 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2817 then when the incrementor becomes less than 1/N, where N is the
2818 mumber of samples collected (and thus proportional to the data
2819 collection time, hence '1 over t'), then the Wang-Lambda
2820 incrementor is set to 1/N, decreasing every step. Once this occurs,
2821 :mdp:`wl-ratio` is ignored, but the weights will still stop
2822 updating when the equilibration criteria set in
2823 :mdp:`lmc-weights-equil` is achieved.
2825 .. mdp:: lmc-repeats
2828 Controls the number of times that each Monte Carlo swap type is
2829 performed each iteration. In the limit of large numbers of Monte
2830 Carlo repeats, then all methods converge to Gibbs sampling. The
2831 value will generally not need to be different from 1.
2833 .. mdp:: lmc-gibbsdelta
2836 Limit Gibbs sampling to selected numbers of neighboring states. For
2837 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2838 sampling over all of the states that are defined. A positive value
2839 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2840 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2841 value of -1 means that all states are considered. For less than 100
2842 states, it is probably not that expensive to include all states.
2844 .. mdp:: lmc-forced-nstart
2847 Force initial state space sampling to generate weights. In order to
2848 come up with reasonable initial weights, this setting allows the
2849 simulation to drive from the initial to the final lambda state,
2850 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2851 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2852 sufficiently long (thousands of steps, perhaps), then the weights
2853 will be close to correct. However, in most cases, it is probably
2854 better to simply run the standard weight equilibration algorithms.
2856 .. mdp:: nst-transition-matrix
2859 Frequency of outputting the expanded ensemble transition matrix. A
2860 negative number means it will only be printed at the end of the
2863 .. mdp:: symmetrized-transition-matrix
2866 Whether to symmetrize the empirical transition matrix. In the
2867 infinite limit the matrix will be symmetric, but will diverge with
2868 statistical noise for short timescales. Forced symmetrization, by
2869 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2870 like the existence of (small magnitude) negative eigenvalues.
2872 .. mdp:: mininum-var-min
2875 The min-variance strategy (option of :mdp:`lmc-stats` is only
2876 valid for larger number of samples, and can get stuck if too few
2877 samples are used at each state. :mdp:`mininum-var-min` is the
2878 minimum number of samples that each state that are allowed before
2879 the min-variance strategy is activated if selected.
2881 .. mdp:: init-lambda-weights
2883 The initial weights (free energies) used for the expanded ensemble
2884 states. Default is a vector of zero weights. format is similar to
2885 the lambda vector settings in :mdp:`fep-lambdas`, except the
2886 weights can be any floating point number. Units are kT. Its length
2887 must match the lambda vector lengths.
2889 .. mdp:: lmc-weights-equil
2893 Expanded ensemble weights continue to be updated throughout the
2898 The input expanded ensemble weights are treated as equilibrated,
2899 and are not updated throughout the simulation.
2901 .. mdp-value:: wl-delta
2903 Expanded ensemble weight updating is stopped when the
2904 Wang-Landau incrementor falls below this value.
2906 .. mdp-value:: number-all-lambda
2908 Expanded ensemble weight updating is stopped when the number of
2909 samples at all of the lambda states is greater than this value.
2911 .. mdp-value:: number-steps
2913 Expanded ensemble weight updating is stopped when the number of
2914 steps is greater than the level specified by this value.
2916 .. mdp-value:: number-samples
2918 Expanded ensemble weight updating is stopped when the number of
2919 total samples across all lambda states is greater than the level
2920 specified by this value.
2922 .. mdp-value:: count-ratio
2924 Expanded ensemble weight updating is stopped when the ratio of
2925 samples at the least sampled lambda state and most sampled
2926 lambda state greater than this value.
2928 .. mdp:: simulated-tempering
2931 Turn simulated tempering on or off. Simulated tempering is
2932 implemented as expanded ensemble sampling with different
2933 temperatures instead of different Hamiltonians.
2935 .. mdp:: sim-temp-low
2938 Low temperature for simulated tempering.
2940 .. mdp:: sim-temp-high
2943 High temperature for simulated tempering.
2945 .. mdp:: simulated-tempering-scaling
2947 Controls the way that the temperatures at intermediate lambdas are
2948 calculated from the :mdp:`temperature-lambdas` part of the lambda
2951 .. mdp-value:: linear
2953 Linearly interpolates the temperatures using the values of
2954 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2955 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2956 a temperature of 350. A nonlinear set of temperatures can always
2957 be implemented with uneven spacing in lambda.
2959 .. mdp-value:: geometric
2961 Interpolates temperatures geometrically between
2962 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2963 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2964 :mdp:`sim-temp-low`) raised to the power of
2965 (i/(ntemps-1)). This should give roughly equal exchange for
2966 constant heat capacity, though of course things simulations that
2967 involve protein folding have very high heat capacity peaks.
2969 .. mdp-value:: exponential
2971 Interpolates temperatures exponentially between
2972 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2973 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2974 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2975 (i))-1)/(exp(1.0)-i)).
2983 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2984 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2985 specifies for which dimension(s) the freezing applies. To avoid
2986 spurious contributions to the virial and pressure due to large
2987 forces between completely frozen atoms you need to use energy group
2988 exclusions, this also saves computing time. Note that coordinates
2989 of frozen atoms are not scaled by pressure-coupling algorithms.
2993 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2994 specify ``Y`` or ``N`` for X, Y and Z and for each group (*e.g.*
2995 ``Y Y N N N N`` means that particles in the first group can move only in
2996 Z direction. The particles in the second group can move in any
2999 .. mdp:: cos-acceleration
3001 (0) [nm ps\ :sup:`-2`]
3002 the amplitude of the acceleration profile for calculating the
3003 viscosity. The acceleration is in the X-direction and the magnitude
3004 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
3005 added to the energy file: the amplitude of the velocity profile and
3010 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
3011 The velocities of deformation for the box elements: a(x) b(y) c(z)
3012 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
3013 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
3014 elements are corrected for periodicity. The coordinates are
3015 transformed accordingly. Frozen degrees of freedom are (purposely)
3016 also transformed. The time ts is set to t at the first step and at
3017 steps at which x and v are written to trajectory to ensure exact
3018 restarts. Deformation can be used together with semiisotropic or
3019 anisotropic pressure coupling when the appropriate
3020 compressibilities are set to zero. The diagonal elements can be
3021 used to strain a solid. The off-diagonal elements can be used to
3022 shear a solid or a liquid.
3028 .. mdp:: electric-field-x
3029 .. mdp:: electric-field-y
3030 .. mdp:: electric-field-z
3032 Here you can specify an electric field that optionally can be
3033 alternating and pulsed. The general expression for the field
3034 has the form of a gaussian laser pulse:
3036 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
3038 For example, the four parameters for direction x are set in the
3039 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
3040 and ``electric-field-z``) like
3042 ``electric-field-x = E0 omega t0 sigma``
3044 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
3046 In the special case that ``sigma = 0``, the exponential term is omitted
3047 and only the cosine term is used. In this case, ``t0`` must be set to 0.
3048 If also ``omega = 0`` a static electric field is applied.
3050 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
3053 Mixed quantum/classical molecular dynamics
3054 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3058 groups to be descibed at the QM level for MiMiC QM/MM
3064 QM/MM is no longer supported via these .mdp options. For MiMic, use no here.
3066 Computational Electrophysiology
3067 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3068 Use these options to switch on and control ion/water position exchanges in "Computational
3069 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3075 Do not enable ion/water position exchanges.
3077 .. mdp-value:: X ; Y ; Z
3079 Allow for ion/water position exchanges along the chosen direction.
3080 In a typical setup with the membranes parallel to the x-y plane,
3081 ion/water pairs need to be exchanged in Z direction to sustain the
3082 requested ion concentrations in the compartments.
3084 .. mdp:: swap-frequency
3086 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3087 per compartment are determined and exchanges made if necessary.
3088 Normally it is not necessary to check at every time step.
3089 For typical Computational Electrophysiology setups, a value of about 100 is
3090 sufficient and yields a negligible performance impact.
3092 .. mdp:: split-group0
3094 Name of the index group of the membrane-embedded part of channel #0.
3095 The center of mass of these atoms defines one of the compartment boundaries
3096 and should be chosen such that it is near the center of the membrane.
3098 .. mdp:: split-group1
3100 Channel #1 defines the position of the other compartment boundary.
3102 .. mdp:: massw-split0
3104 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3108 Use the geometrical center.
3112 Use the center of mass.
3114 .. mdp:: massw-split1
3116 (no) As above, but for split-group #1.
3118 .. mdp:: solvent-group
3120 Name of the index group of solvent molecules.
3122 .. mdp:: coupl-steps
3124 (10) Average the number of ions per compartment over these many swap attempt steps.
3125 This can be used to prevent that ions near a compartment boundary
3126 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3130 (1) The number of different ion types to be controlled. These are during the
3131 simulation exchanged with solvent molecules to reach the desired reference numbers.
3133 .. mdp:: iontype0-name
3135 Name of the first ion type.
3137 .. mdp:: iontype0-in-A
3139 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3140 The default value of -1 means: use the number of ions as found in time step 0
3143 .. mdp:: iontype0-in-B
3145 (-1) Reference number of ions of type 0 for compartment B.
3147 .. mdp:: bulk-offsetA
3149 (0.0) Offset of the first swap layer from the compartment A midplane.
3150 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3151 at maximum distance (= bulk concentration) to the split group layers. However,
3152 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3153 towards one of the compartment-partitioning layers (at +/- 1.0).
3155 .. mdp:: bulk-offsetB
3157 (0.0) Offset of the other swap layer from the compartment B midplane.
3162 (\1) Only swap ions if threshold difference to requested count is reached.
3166 (2.0) [nm] Radius of the split cylinder #0.
3167 Two split cylinders (mimicking the channel pores) can optionally be defined
3168 relative to the center of the split group. With the help of these cylinders
3169 it can be counted which ions have passed which channel. The split cylinder
3170 definition has no impact on whether or not ion/water swaps are done.
3174 (1.0) [nm] Upper extension of the split cylinder #0.
3178 (1.0) [nm] Lower extension of the split cylinder #0.
3182 (2.0) [nm] Radius of the split cylinder #1.
3186 (1.0) [nm] Upper extension of the split cylinder #1.
3190 (1.0) [nm] Lower extension of the split cylinder #1.
3192 Density-guided simulations
3193 ^^^^^^^^^^^^^^^^^^^^^^^^^^
3195 These options enable and control the calculation and application of additional
3196 forces that are derived from three-dimensional densities, e.g., from cryo
3197 electron-microscopy experiments. (See the `reference manual`_ for details)
3199 .. mdp:: density-guided-simulation-active
3201 (no) Activate density-guided simulations.
3203 .. mdp:: density-guided-simulation-group
3205 (protein) The atoms that are subject to the forces from the density-guided
3206 simulation and contribute to the simulated density.
3208 .. mdp:: density-guided-simulation-similarity-measure
3210 (inner-product) Similarity measure between the density that is calculated
3211 from the atom positions and the reference density.
3213 .. mdp-value:: inner-product
3215 Takes the sum of the product of reference density and simulated density
3218 .. mdp-value:: relative-entropy
3220 Uses the negative relative entropy (or Kullback-Leibler divergence)
3221 between reference density and simulated density as similarity measure.
3222 Negative density values are ignored.
3224 .. mdp-value:: cross-correlation
3226 Uses the Pearson correlation coefficient between reference density and
3227 simulated density as similarity measure.
3229 .. mdp:: density-guided-simulation-atom-spreading-weight
3231 (unity) Determines the multiplication factor for the Gaussian kernel when
3232 spreading atoms on the grid.
3234 .. mdp-value:: unity
3236 Every atom in the density fitting group is assigned the same unit factor.
3240 Atoms contribute to the simulated density proportional to their mass.
3242 .. mdp-value:: charge
3244 Atoms contribute to the simulated density proportional to their charge.
3246 .. mdp:: density-guided-simulation-force-constant
3248 (1e+09) [kJ mol\ :sup:`-1`] The scaling factor for density-guided simulation
3249 forces. May also be negative.
3251 .. mdp:: density-guided-simulation-gaussian-transform-spreading-width
3253 (0.2) [nm] The Gaussian RMS width for the spread kernel for the simulated
3256 .. mdp:: density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width
3258 (4) The range after which the gaussian is cut off in multiples of the Gaussian
3259 RMS width described above.
3261 .. mdp:: density-guided-simulation-reference-density-filename
3263 (reference.mrc) Reference density file name using an absolute path or a path
3264 relative to the to the folder from which :ref:`gmx mdrun` is called.
3266 .. mdp:: density-guided-simulation-nst
3268 (1) Interval in steps at which the density fitting forces are evaluated
3269 and applied. The forces are scaled by this number when applied (See the
3270 `reference manual`_ for details).
3272 .. mdp:: density-guided-simulation-normalize-densities
3274 (true) Normalize the sum of density voxel values to one for the reference
3275 density as well as the simulated density.
3277 .. mdp:: density-guided-simulation-adaptive-force-scaling
3279 (false) Adapt the force constant to ensure a steady increase in similarity
3280 between simulated and reference density.
3284 Do not use adaptive force scaling.
3288 Use adaptive force scaling.
3290 .. mdp:: density-guided-simulation-adaptive-force-scaling-time-constant
3292 (4) [ps] Couple force constant to increase in similarity with reference density
3293 with this time constant. Larger times result in looser coupling.
3295 .. mdp:: density-guided-simulation-shift-vector
3297 (0,0,0) [nm] Add this vector to all atoms in the
3298 density-guided-simulation-group before calculating forces and energies for
3299 density-guided-simulations. Affects only the density-guided-simulation forces
3300 and energies. Corresponds to a shift of the input density in the opposite
3301 direction by (-1) * density-guided-simulation-shift-vector.
3303 .. mdp:: density-guided-simulation-transformation-matrix
3305 (1,0,0,0,1,0,0,0,1) Multiply all atoms with this matrix in the
3306 density-guided-simulation-group before calculating forces and energies for
3307 density-guided-simulations. Affects only the density-guided-simulation forces
3308 and energies. Corresponds to a transformation of the input density by the
3309 inverse of this matrix. The matrix is given in row-major order.
3310 This option allows, e.g., rotation of the density-guided atom group around the
3311 z-axis by :math:`\theta` degress by using following input:
3312 :math:`(\cos \theta , -\sin \theta , 0 , \sin \theta , \cos \theta , 0 , 0 , 0 , 1)` .
3314 User defined thingies
3315 ^^^^^^^^^^^^^^^^^^^^^
3319 .. mdp:: userint1 (0)
3320 .. mdp:: userint2 (0)
3321 .. mdp:: userint3 (0)
3322 .. mdp:: userint4 (0)
3323 .. mdp:: userreal1 (0)
3324 .. mdp:: userreal2 (0)
3325 .. mdp:: userreal3 (0)
3326 .. mdp:: userreal4 (0)
3328 These you can use if you modify code. You can pass integers and
3329 reals and groups to your subroutine. Check the inputrec definition
3330 in ``src/gromacs/mdtypes/inputrec.h``
3335 These features have been removed from |Gromacs|, but so that old
3336 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3337 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3338 fatal error if this is set.
3344 .. mdp:: implicit-solvent
3348 .. _reference manual: gmx-manual-parent-dir_