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.
499 The neighbor list is only constructed once and never
500 updated. This is mainly useful for vacuum simulations in which
501 all particles see each other. But vacuum simulations are
502 (temporarily) not supported.
512 Use periodic boundary conditions in all directions.
516 Use no periodic boundary conditions, ignore the box. To simulate
517 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
518 best performance without cut-offs on a single MPI rank, set
519 :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`.
523 Use periodic boundary conditions in x and y directions
524 only. This works only with :mdp-value:`ns-type=grid` and can be used
525 in combination with walls_. Without walls or with only one wall
526 the system size is infinite in the z direction. Therefore
527 pressure coupling or Ewald summation methods can not be
528 used. These disadvantages do not apply when two walls are used.
530 .. mdp:: periodic-molecules
534 molecules are finite, fast molecular PBC can be used
538 for systems with molecules that couple to themselves through the
539 periodic boundary conditions, this requires a slower PBC
540 algorithm and molecules are not made whole in the output
542 .. mdp:: verlet-buffer-tolerance
544 (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
546 Used when performing a simulation with dynamics. This sets
547 the maximum allowed error for pair interactions per particle caused
548 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
549 :mdp:`nstlist` and the Verlet buffer size are fixed (for
550 performance reasons), particle pairs not in the pair list can
551 occasionally get within the cut-off distance during
552 :mdp:`nstlist` -1 steps. This causes very small jumps in the
553 energy. In a constant-temperature ensemble, these very small energy
554 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
555 estimate assumes a homogeneous particle distribution, hence the
556 errors might be slightly underestimated for multi-phase
557 systems. (See the `reference manual`_ for details). For longer
558 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
559 overestimated, because the interactions between particles are
560 ignored. Combined with cancellation of errors, the actual drift of
561 the total energy is usually one to two orders of magnitude
562 smaller. Note that the generated buffer size takes into account
563 that the |Gromacs| pair-list setup leads to a reduction in the
564 drift by a factor 10, compared to a simple particle-pair based
565 list. Without dynamics (energy minimization etc.), the buffer is 5%
566 of the cut-off. For NVE simulations the initial temperature is
567 used, unless this is zero, in which case a buffer of 10% is
568 used. For NVE simulations the tolerance usually needs to be lowered
569 to achieve proper energy conservation on the nanosecond time
570 scale. To override the automated buffer setting, use
571 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
576 Cut-off distance for the short-range neighbor list. With dynamics,
577 this is by default set by the :mdp:`verlet-buffer-tolerance` option
578 and the value of :mdp:`rlist` is ignored. Without dynamics, this
579 is by default set to the maximum cut-off plus 5% buffer, except
580 for test particle insertion, where the buffer is managed exactly
581 and automatically. For NVE simulations, where the automated
582 setting is not possible, the advised procedure is to run :ref:`gmx grompp`
583 with an NVT setup with the expected temperature and copy the resulting
584 value of :mdp:`rlist` to the NVE setup.
592 .. mdp-value:: Cut-off
594 Plain cut-off with pair list radius :mdp:`rlist` and
595 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
600 Classical Ewald sum electrostatics. The real-space cut-off
601 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
602 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
603 of wave vectors used in reciprocal space is controlled by
604 :mdp:`fourierspacing`. The relative accuracy of
605 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
607 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
608 large systems. It is included mainly for reference - in most
609 cases PME will perform much better.
613 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
614 space is similar to the Ewald sum, while the reciprocal part is
615 performed with FFTs. Grid dimensions are controlled with
616 :mdp:`fourierspacing` and the interpolation order with
617 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
618 interpolation the electrostatic forces have an accuracy of
619 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
620 this you might try 0.15 nm. When running in parallel the
621 interpolation parallelizes better than the FFT, so try
622 decreasing grid dimensions while increasing interpolation.
624 .. mdp-value:: P3M-AD
626 Particle-Particle Particle-Mesh algorithm with analytical
627 derivative for for long range electrostatic interactions. The
628 method and code is identical to SPME, except that the influence
629 function is optimized for the grid. This gives a slight increase
632 .. mdp-value:: Reaction-Field
634 Reaction field electrostatics with Coulomb cut-off
635 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
636 dielectric constant beyond the cut-off is
637 :mdp:`epsilon-rf`. The dielectric constant can be set to
638 infinity by setting :mdp:`epsilon-rf` =0.
642 Currently unsupported.
643 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
644 with user-defined potential functions for repulsion, dispersion
645 and Coulomb. When pair interactions are present, :ref:`gmx
646 mdrun` also expects to find a file ``tablep.xvg`` for the pair
647 interactions. When the same interactions should be used for
648 non-bonded and pair interactions the user can specify the same
649 file name for both table files. These files should contain 7
650 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
651 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
652 function, ``g(x)`` the dispersion function and ``h(x)`` the
653 repulsion function. When :mdp:`vdwtype` is not set to User the
654 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
655 the non-bonded interactions ``x`` values should run from 0 to
656 the largest cut-off distance + :mdp:`table-extension` and
657 should be uniformly spaced. For the pair interactions the table
658 length in the file will be used. The optimal spacing, which is
659 used for non-user tables, is ``0.002 nm`` when you run in mixed
660 precision or ``0.0005 nm`` when you run in double precision. The
661 function value at ``x=0`` is not important. More information is
662 in the printed manual.
664 .. mdp-value:: PME-Switch
666 Currently unsupported.
667 A combination of PME and a switch function for the direct-space
668 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
671 .. mdp-value:: PME-User
673 Currently unsupported.
674 A combination of PME and user tables (see
675 above). :mdp:`rcoulomb` is allowed to be smaller than
676 :mdp:`rlist`. The PME mesh contribution is subtracted from the
677 user table by :ref:`gmx mdrun`. Because of this subtraction the
678 user tables should contain about 10 decimal places.
680 .. mdp-value:: PME-User-Switch
682 Currently unsupported.
683 A combination of PME-User and a switching function (see
684 above). The switching function is applied to final
685 particle-particle interaction, *i.e.* both to the user supplied
686 function and the PME Mesh correction part.
688 .. mdp:: coulomb-modifier
690 .. mdp-value:: Potential-shift
692 Shift the Coulomb potential by a constant such that it is zero
693 at the cut-off. This makes the potential the integral of the
694 force. Note that this does not affect the forces or the
699 Use an unmodified Coulomb potential. This can be useful
700 when comparing energies with those computed with other software.
702 .. mdp:: rcoulomb-switch
705 where to start switching the Coulomb potential, only relevant
706 when force or potential switching is used
711 The distance for the Coulomb cut-off. Note that with PME this value
712 can be increased by the PME tuning in :ref:`gmx mdrun` along with
713 the PME grid spacing.
718 The relative dielectric constant. A value of 0 means infinity.
723 The relative dielectric constant of the reaction field. This
724 is only used with reaction-field electrostatics. A value of 0
733 .. mdp-value:: Cut-off
735 Plain cut-off with pair list radius :mdp:`rlist` and VdW
736 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
740 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
741 grid dimensions are controlled with :mdp:`fourierspacing` in
742 the same way as for electrostatics, and the interpolation order
743 is controlled with :mdp:`pme-order`. The relative accuracy of
744 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
745 and the specific combination rules that are to be used by the
746 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
750 This functionality is deprecated and replaced by using
751 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
752 The LJ (not Buckingham) potential is decreased over the whole range and
753 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
756 .. mdp-value:: Switch
758 This functionality is deprecated and replaced by using
759 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
760 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
761 which it is switched off to reach zero at :mdp:`rvdw`. Both the
762 potential and force functions are continuously smooth, but be
763 aware that all switch functions will give rise to a bulge
764 (increase) in the force (since we are switching the
769 Currently unsupported.
770 See user for :mdp:`coulombtype`. The function value at zero is
771 not important. When you want to use LJ correction, make sure
772 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
773 function. When :mdp:`coulombtype` is not set to User the values
774 for the ``f`` and ``-f'`` columns are ignored.
776 .. mdp:: vdw-modifier
778 .. mdp-value:: Potential-shift
780 Shift the Van der Waals potential by a constant such that it is
781 zero at the cut-off. This makes the potential the integral of
782 the force. Note that this does not affect the forces or the
787 Use an unmodified Van der Waals potential. This can be useful
788 when comparing energies with those computed with other software.
790 .. mdp-value:: Force-switch
792 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
793 and :mdp:`rvdw`. This shifts the potential shift over the whole
794 range and switches it to zero at the cut-off. Note that this is
795 more expensive to calculate than a plain cut-off and it is not
796 required for energy conservation, since Potential-shift
797 conserves energy just as well.
799 .. mdp-value:: Potential-switch
801 Smoothly switches the potential to zero between
802 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
803 articifically large forces in the switching region and is much
804 more expensive to calculate. This option should only be used if
805 the force field you are using requires this.
810 where to start switching the LJ force and possibly the potential,
811 only relevant when force or potential switching is used
816 distance for the LJ or Buckingham cut-off
822 don't apply any correction
824 .. mdp-value:: EnerPres
826 apply long range dispersion corrections for Energy and Pressure
830 apply long range dispersion corrections for Energy only
836 .. mdp:: table-extension
839 Extension of the non-bonded potential lookup tables beyond the
840 largest cut-off distance. With actual non-bonded interactions
841 the tables are never accessed beyond the cut-off. But a longer
842 table length might be needed for the 1-4 interactions, which
843 are always tabulated irrespective of the use of tables for
844 the non-bonded interactions.
846 .. mdp:: energygrp-table
848 Currently unsupported.
849 When user tables are used for electrostatics and/or VdW, here one
850 can give pairs of energy groups for which seperate user tables
851 should be used. The two energy groups will be appended to the table
852 file name, in order of their definition in :mdp:`energygrps`,
853 seperated by underscores. For example, if ``energygrps = Na Cl
854 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
855 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
856 normal ``table.xvg`` which will be used for all other energy group
863 .. mdp:: fourierspacing
866 For ordinary Ewald, the ratio of the box dimensions and the spacing
867 determines a lower bound for the number of wave vectors to use in
868 each (signed) direction. For PME and P3M, that ratio determines a
869 lower bound for the number of Fourier-space grid points that will
870 be used along that axis. In all cases, the number for each
871 direction can be overridden by entering a non-zero value for that
872 :mdp:`fourier-nx` direction. For optimizing the relative load of
873 the particle-particle interactions and the mesh part of PME, it is
874 useful to know that the accuracy of the electrostatics remains
875 nearly constant when the Coulomb cut-off and the PME grid spacing
876 are scaled by the same factor. Note that this spacing can be scaled
877 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
884 Highest magnitude of wave vectors in reciprocal space when using Ewald.
885 Grid size when using PME or P3M. These values override
886 :mdp:`fourierspacing` per direction. The best choice is powers of
887 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
888 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
894 Interpolation order for PME. 4 equals cubic interpolation. You
895 might try 6/8/10 when running in parallel and simultaneously
896 decrease grid dimension.
901 The relative strength of the Ewald-shifted direct potential at
902 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
903 will give a more accurate direct sum, but then you need more wave
904 vectors for the reciprocal sum.
906 .. mdp:: ewald-rtol-lj
909 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
910 to control the relative strength of the dispersion potential at
911 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
912 electrostatic potential.
914 .. mdp:: lj-pme-comb-rule
917 The combination rules used to combine VdW-parameters in the
918 reciprocal part of LJ-PME. Geometric rules are much faster than
919 Lorentz-Berthelot and usually the recommended choice, even when the
920 rest of the force field uses the Lorentz-Berthelot rules.
922 .. mdp-value:: Geometric
924 Apply geometric combination rules
926 .. mdp-value:: Lorentz-Berthelot
928 Apply Lorentz-Berthelot combination rules
930 .. mdp:: ewald-geometry
934 The Ewald sum is performed in all three dimensions.
938 The reciprocal sum is still performed in 3D, but a force and
939 potential correction applied in the ``z`` dimension to produce a
940 pseudo-2D summation. If your system has a slab geometry in the
941 ``x-y`` plane you can try to increase the ``z``-dimension of the box
942 (a box height of 3 times the slab height is usually ok) and use
945 .. mdp:: epsilon-surface
948 This controls the dipole correction to the Ewald summation in
949 3D. The default value of zero means it is turned off. Turn it on by
950 setting it to the value of the relative permittivity of the
951 imaginary surface around your infinite system. Be careful - you
952 shouldn't use this if you have free mobile charges in your
953 system. This value does not affect the slab 3DC variant of the long
964 No temperature coupling.
966 .. mdp-value:: berendsen
968 Temperature coupling with a Berendsen thermostat to a bath with
969 temperature :mdp:`ref-t`, with time constant
970 :mdp:`tau-t`. Several groups can be coupled separately, these
971 are specified in the :mdp:`tc-grps` field separated by spaces.
973 .. mdp-value:: nose-hoover
975 Temperature coupling using a Nose-Hoover extended ensemble. The
976 reference temperature and coupling groups are selected as above,
977 but in this case :mdp:`tau-t` controls the period of the
978 temperature fluctuations at equilibrium, which is slightly
979 different from a relaxation time. For NVT simulations the
980 conserved energy quantity is written to the energy and log files.
982 .. mdp-value:: andersen
984 Temperature coupling by randomizing a fraction of the particle velocities
985 at each timestep. Reference temperature and coupling groups are
986 selected as above. :mdp:`tau-t` is the average time between
987 randomization of each molecule. Inhibits particle dynamics
988 somewhat, but little or no ergodicity issues. Currently only
989 implemented with velocity Verlet, and not implemented with
992 .. mdp-value:: andersen-massive
994 Temperature coupling by randomizing velocities of all particles at
995 infrequent timesteps. Reference temperature and coupling groups are
996 selected as above. :mdp:`tau-t` is the time between
997 randomization of all molecules. Inhibits particle dynamics
998 somewhat, but little or no ergodicity issues. Currently only
999 implemented with velocity Verlet.
1001 .. mdp-value:: v-rescale
1003 Temperature coupling using velocity rescaling with a stochastic
1004 term (JCP 126, 014101). This thermostat is similar to Berendsen
1005 coupling, with the same scaling using :mdp:`tau-t`, but the
1006 stochastic term ensures that a proper canonical ensemble is
1007 generated. The random seed is set with :mdp:`ld-seed`. This
1008 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1009 simulations the conserved energy quantity is written to the
1010 energy and log file.
1015 The frequency for coupling the temperature. The default value of -1
1016 sets :mdp:`nsttcouple` equal to 10, or fewer steps if required
1017 for accurate integration. Note that the default value is not 1
1018 because additional computation and communication is required for
1019 obtaining the kinetic energy. For velocity
1020 Verlet integrators :mdp:`nsttcouple` is set to 1.
1022 .. mdp:: nh-chain-length
1025 The number of chained Nose-Hoover thermostats for velocity Verlet
1026 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1027 only supports 1. Data for the NH chain variables is not printed
1028 to the :ref:`edr` file by default, but can be turned on with the
1029 :mdp:`print-nose-hoover-chain-variables` option.
1031 .. mdp:: print-nose-hoover-chain-variables
1035 Do not store Nose-Hoover chain variables in the energy file.
1039 Store all positions and velocities of the Nose-Hoover chain
1044 groups to couple to separate temperature baths
1049 time constant for coupling (one for each group in
1050 :mdp:`tc-grps`), -1 means no temperature coupling
1055 reference temperature for coupling (one for each group in
1066 No pressure coupling. This means a fixed box size.
1068 .. mdp-value:: Berendsen
1070 Exponential relaxation pressure coupling with time constant
1071 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1072 argued that this does not yield a correct thermodynamic
1073 ensemble, but it is the most efficient way to scale a box at the
1076 .. mdp-value:: C-rescale
1078 Exponential relaxation pressure coupling with time constant
1079 :mdp:`tau-p`, including a stochastic term to enforce correct
1080 volume fluctuations. The box is scaled every :mdp:`nstpcouple`
1081 steps. It can be used for both equilibration and production.
1083 .. mdp-value:: Parrinello-Rahman
1085 Extended-ensemble pressure coupling where the box vectors are
1086 subject to an equation of motion. The equation of motion for the
1087 atoms is coupled to this. No instantaneous scaling takes
1088 place. As for Nose-Hoover temperature coupling the time constant
1089 :mdp:`tau-p` is the period of pressure fluctuations at
1090 equilibrium. This is probably a better method when you want to
1091 apply pressure scaling during data collection, but beware that
1092 you can get very large oscillations if you are starting from a
1093 different pressure. For simulations where the exact fluctations
1094 of the NPT ensemble are important, or if the pressure coupling
1095 time is very short it may not be appropriate, as the previous
1096 time step pressure is used in some steps of the |Gromacs|
1097 implementation for the current time step pressure.
1101 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1102 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1103 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1104 time constant :mdp:`tau-p` is the period of pressure
1105 fluctuations at equilibrium. This is probably a better method
1106 when you want to apply pressure scaling during data collection,
1107 but beware that you can get very large oscillations if you are
1108 starting from a different pressure. Currently (as of version
1109 5.1), it only supports isotropic scaling, and only works without
1114 Specifies the kind of isotropy of the pressure coupling used. Each
1115 kind takes one or more values for :mdp:`compressibility` and
1116 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1118 .. mdp-value:: isotropic
1120 Isotropic pressure coupling with time constant
1121 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1122 :mdp:`ref-p` is required.
1124 .. mdp-value:: semiisotropic
1126 Pressure coupling which is isotropic in the ``x`` and ``y``
1127 direction, but different in the ``z`` direction. This can be
1128 useful for membrane simulations. Two values each for
1129 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1130 ``x/y`` and ``z`` directions respectively.
1132 .. mdp-value:: anisotropic
1134 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1135 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1136 respectively. When the off-diagonal compressibilities are set to
1137 zero, a rectangular box will stay rectangular. Beware that
1138 anisotropic scaling can lead to extreme deformation of the
1141 .. mdp-value:: surface-tension
1143 Surface tension coupling for surfaces parallel to the
1144 xy-plane. Uses normal pressure coupling for the ``z``-direction,
1145 while the surface tension is coupled to the ``x/y`` dimensions of
1146 the box. The first :mdp:`ref-p` value is the reference surface
1147 tension times the number of surfaces ``bar nm``, the second
1148 value is the reference ``z``-pressure ``bar``. The two
1149 :mdp:`compressibility` values are the compressibility in the
1150 ``x/y`` and ``z`` direction respectively. The value for the
1151 ``z``-compressibility should be reasonably accurate since it
1152 influences the convergence of the surface-tension, it can also
1153 be set to zero to have a box with constant height.
1158 The frequency for coupling the pressure. The default value of -1
1159 sets :mdp:`nstpcouple` equal to 10, or fewer steps if required
1160 for accurate integration. Note that the default value is not 1
1161 because additional computation and communication is required for
1162 obtaining the virial. For velocity
1163 Verlet integrators :mdp:`nstpcouple` is set to 1.
1168 The time constant for pressure coupling (one value for all
1171 .. mdp:: compressibility
1174 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1175 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1176 required values is implied by :mdp:`pcoupltype`.
1181 The reference pressure for coupling. The number of required values
1182 is implied by :mdp:`pcoupltype`.
1184 .. mdp:: refcoord-scaling
1188 The reference coordinates for position restraints are not
1189 modified. Note that with this option the virial and pressure
1190 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1195 The reference coordinates are scaled with the scaling matrix of
1196 the pressure coupling.
1200 Scale the center of mass of the reference coordinates with the
1201 scaling matrix of the pressure coupling. The vectors of each
1202 reference coordinate to the center of mass are not scaled. Only
1203 one COM is used, even when there are multiple molecules with
1204 position restraints. For calculating the COM of the reference
1205 coordinates in the starting configuration, periodic boundary
1206 conditions are not taken into account. Note that with this option
1207 the virial and pressure might be ill defined, see
1208 :ref:`here <reference-manual-position-restraints>` for more details.
1214 Simulated annealing is controlled separately for each temperature
1215 group in |Gromacs|. The reference temperature is a piecewise linear
1216 function, but you can use an arbitrary number of points for each
1217 group, and choose either a single sequence or a periodic behaviour for
1218 each group. The actual annealing is performed by dynamically changing
1219 the reference temperature used in the thermostat algorithm selected,
1220 so remember that the system will usually not instantaneously reach the
1221 reference temperature!
1225 Type of annealing for each temperature group
1229 No simulated annealing - just couple to reference temperature value.
1231 .. mdp-value:: single
1233 A single sequence of annealing points. If your simulation is
1234 longer than the time of the last point, the temperature will be
1235 coupled to this constant value after the annealing sequence has
1236 reached the last time point.
1238 .. mdp-value:: periodic
1240 The annealing will start over at the first reference point once
1241 the last reference time is reached. This is repeated until the
1244 .. mdp:: annealing-npoints
1246 A list with the number of annealing reference/control points used
1247 for each temperature group. Use 0 for groups that are not
1248 annealed. The number of entries should equal the number of
1251 .. mdp:: annealing-time
1253 List of times at the annealing reference/control points for each
1254 group. If you are using periodic annealing, the times will be used
1255 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1256 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1257 etc. The number of entries should equal the sum of the numbers
1258 given in :mdp:`annealing-npoints`.
1260 .. mdp:: annealing-temp
1262 List of temperatures at the annealing reference/control points for
1263 each group. The number of entries should equal the sum of the
1264 numbers given in :mdp:`annealing-npoints`.
1266 Confused? OK, let's use an example. Assume you have two temperature
1267 groups, set the group selections to ``annealing = single periodic``,
1268 the number of points of each group to ``annealing-npoints = 3 4``, the
1269 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1270 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1271 will be coupled to 298K at 0ps, but the reference temperature will
1272 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1273 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1274 second group is coupled to 298K at 0ps, it increases linearly to 320K
1275 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1276 decreases to 298K, and then it starts over with the same pattern
1277 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1278 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1288 Do not generate velocities. The velocities are set to zero
1289 when there are no velocities in the input structure file.
1293 Generate velocities in :ref:`gmx grompp` according to a
1294 Maxwell distribution at temperature :mdp:`gen-temp`, with
1295 random seed :mdp:`gen-seed`. This is only meaningful with
1296 :mdp-value:`integrator=md`.
1301 temperature for Maxwell distribution
1306 used to initialize random generator for random velocities,
1307 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1314 .. mdp:: constraints
1316 Controls which bonds in the topology will be converted to rigid
1317 holonomic constraints. Note that typical rigid water models do not
1318 have bonds, but rather a specialized ``[settles]`` directive, so
1319 are not affected by this keyword.
1323 No bonds converted to constraints.
1325 .. mdp-value:: h-bonds
1327 Convert the bonds with H-atoms to constraints.
1329 .. mdp-value:: all-bonds
1331 Convert all bonds to constraints.
1333 .. mdp-value:: h-angles
1335 Convert all bonds to constraints and convert the angles that
1336 involve H-atoms to bond-constraints.
1338 .. mdp-value:: all-angles
1340 Convert all bonds to constraints and all angles to bond-constraints.
1342 .. mdp:: constraint-algorithm
1344 Chooses which solver satisfies any non-SETTLE holonomic
1347 .. mdp-value:: LINCS
1349 LINear Constraint Solver. With domain decomposition the parallel
1350 version P-LINCS is used. The accuracy in set with
1351 :mdp:`lincs-order`, which sets the number of matrices in the
1352 expansion for the matrix inversion. After the matrix inversion
1353 correction the algorithm does an iterative correction to
1354 compensate for lengthening due to rotation. The number of such
1355 iterations can be controlled with :mdp:`lincs-iter`. The root
1356 mean square relative constraint deviation is printed to the log
1357 file every :mdp:`nstlog` steps. If a bond rotates more than
1358 :mdp:`lincs-warnangle` in one step, a warning will be printed
1359 both to the log file and to ``stderr``. LINCS should not be used
1360 with coupled angle constraints.
1362 .. mdp-value:: SHAKE
1364 SHAKE is slightly slower and less stable than LINCS, but does
1365 work with angle constraints. The relative tolerance is set with
1366 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1367 does not support constraints between atoms on different
1368 decomposition domains, so it can only be used with domain
1369 decomposition when so-called update-groups are used, which is
1370 usally the case when only bonds involving hydrogens are
1371 constrained. SHAKE can not be used with energy minimization.
1373 .. mdp:: continuation
1375 This option was formerly known as ``unconstrained-start``.
1379 apply constraints to the start configuration and reset shells
1383 do not apply constraints to the start configuration and do not
1384 reset shells, useful for exact coninuation and reruns
1389 relative tolerance for SHAKE
1391 .. mdp:: lincs-order
1394 Highest order in the expansion of the constraint coupling
1395 matrix. When constraints form triangles, an additional expansion of
1396 the same order is applied on top of the normal expansion only for
1397 the couplings within such triangles. For "normal" MD simulations an
1398 order of 4 usually suffices, 6 is needed for large time-steps with
1399 virtual sites or BD. For accurate energy minimization an order of 8
1400 or more might be required. With domain decomposition, the cell size
1401 is limited by the distance spanned by :mdp:`lincs-order` +1
1402 constraints. When one wants to scale further than this limit, one
1403 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1404 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1405 )* :mdp:`lincs-order` remains constant.
1410 Number of iterations to correct for rotational lengthening in
1411 LINCS. For normal runs a single step is sufficient, but for NVE
1412 runs where you want to conserve energy accurately or for accurate
1413 energy minimization you might want to increase it to 2.
1415 .. mdp:: lincs-warnangle
1418 maximum angle that a bond can rotate before LINCS will complain
1424 bonds are represented by a harmonic potential
1428 bonds are represented by a Morse potential
1431 Energy group exclusions
1432 ^^^^^^^^^^^^^^^^^^^^^^^
1434 .. mdp:: energygrp-excl
1436 Pairs of energy groups for which all non-bonded interactions are
1437 excluded. An example: if you have two energy groups ``Protein`` and
1438 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1439 would give only the non-bonded interactions between the protein and
1440 the solvent. This is especially useful for speeding up energy
1441 calculations with ``mdrun -rerun`` and for excluding interactions
1442 within frozen groups.
1451 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1452 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1453 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1454 used (it is usually best to use semiisotropic pressure coupling
1455 with the ``x/y`` compressibility set to 0, as otherwise the surface
1456 area will change). Walls interact wit the rest of the system
1457 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1458 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1459 monitor the interaction of energy groups with each wall. The center
1460 of mass motion removal will be turned off in the ``z``-direction.
1462 .. mdp:: wall-atomtype
1464 the atom type name in the force field for each wall. By (for
1465 example) defining a special wall atom type in the topology with its
1466 own combination rules, this allows for independent tuning of the
1467 interaction of each atomtype with the walls.
1473 LJ integrated over the volume behind the wall: 9-3 potential
1477 LJ integrated over the wall surface: 10-4 potential
1481 direct LJ potential with the ``z`` distance from the wall
1485 user defined potentials indexed with the ``z`` distance from the
1486 wall, the tables are read analogously to the
1487 :mdp:`energygrp-table` option, where the first name is for a
1488 "normal" energy group and the second name is ``wall0`` or
1489 ``wall1``, only the dispersion and repulsion columns are used
1491 .. mdp:: wall-r-linpot
1494 Below this distance from the wall the potential is continued
1495 linearly and thus the force is constant. Setting this option to a
1496 postive value is especially useful for equilibration when some
1497 atoms are beyond a wall. When the value is <=0 (<0 for
1498 :mdp:`wall-type` =table), a fatal error is generated when atoms
1501 .. mdp:: wall-density
1503 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1504 the number density of the atoms for each wall for wall types 9-3
1507 .. mdp:: wall-ewald-zfac
1510 The scaling factor for the third box vector for Ewald summation
1511 only, the minimum is 2. Ewald summation can only be used with
1512 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1513 ``=3dc``. The empty layer in the box serves to decrease the
1514 unphysical Coulomb interaction between periodic images.
1520 Note that where pulling coordinates are applicable, there can be more
1521 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1522 variables will exist accordingly. Documentation references to things
1523 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1524 applicable pulling coordinate, eg. the second pull coordinate is described by
1525 pull-coord2-vec, pull-coord2-k, and so on.
1531 No center of mass pulling. All the following pull options will
1532 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1537 Center of mass pulling will be applied on 1 or more groups using
1538 1 or more pull coordinates.
1540 .. mdp:: pull-cylinder-r
1543 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1545 .. mdp:: pull-constr-tol
1548 the relative constraint tolerance for constraint pulling
1550 .. mdp:: pull-print-com
1554 do not print the COM for any group
1558 print the COM of all groups for all pull coordinates
1560 .. mdp:: pull-print-ref-value
1564 do not print the reference value for each pull coordinate
1568 print the reference value for each pull coordinate
1570 .. mdp:: pull-print-components
1574 only print the distance for each pull coordinate
1578 print the distance and Cartesian components selected in
1579 :mdp:`pull-coord1-dim`
1581 .. mdp:: pull-nstxout
1584 frequency for writing out the COMs of all the pull group (0 is
1587 .. mdp:: pull-nstfout
1590 frequency for writing out the force of all the pulled group
1593 .. mdp:: pull-pbc-ref-prev-step-com
1597 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1598 treatment of periodic boundary conditions.
1602 Use the COM of the previous step as reference for the treatment
1603 of periodic boundary conditions. The reference is initialized
1604 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1605 be located centrally in the group. Using the COM from the
1606 previous step can be useful if one or more pull groups are large.
1608 .. mdp:: pull-xout-average
1612 Write the instantaneous coordinates for all the pulled groups.
1616 Write the average coordinates (since last output) for all the
1617 pulled groups. N.b., some analysis tools might expect instantaneous
1620 .. mdp:: pull-fout-average
1624 Write the instantaneous force for all the pulled groups.
1628 Write the average force (since last output) for all the
1629 pulled groups. N.b., some analysis tools might expect instantaneous
1632 .. mdp:: pull-ngroups
1635 The number of pull groups, not including the absolute reference
1636 group, when used. Pull groups can be reused in multiple pull
1637 coordinates. Below only the pull options for group 1 are given,
1638 further groups simply increase the group index number.
1640 .. mdp:: pull-ncoords
1643 The number of pull coordinates. Below only the pull options for
1644 coordinate 1 are given, further coordinates simply increase the
1645 coordinate index number.
1647 .. mdp:: pull-group1-name
1649 The name of the pull group, is looked up in the index file or in
1650 the default groups to obtain the atoms involved.
1652 .. mdp:: pull-group1-weights
1654 Optional relative weights which are multiplied with the masses of
1655 the atoms to give the total weight for the COM. The number should
1656 be 0, meaning all 1, or the number of atoms in the pull group.
1658 .. mdp:: pull-group1-pbcatom
1661 The reference atom for the treatment of periodic boundary
1662 conditions inside the group (this has no effect on the treatment of
1663 the pbc between groups). This option is only important when the
1664 diameter of the pull group is larger than half the shortest box
1665 vector. For determining the COM, all atoms in the group are put at
1666 their periodic image which is closest to
1667 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1668 atom (number wise) is used, which is only safe for small groups.
1669 :ref:`gmx grompp` checks that the maximum distance from the reference
1670 atom (specifically chosen, or not) to the other atoms in the group
1671 is not too large. This parameter is not used with
1672 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1673 weighting, which is useful for a group of molecules in a periodic
1674 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1677 .. mdp:: pull-coord1-type
1679 .. mdp-value:: umbrella
1681 Center of mass pulling using an umbrella potential between the
1682 reference group and one or more groups.
1684 .. mdp-value:: constraint
1686 Center of mass pulling using a constraint between the reference
1687 group and one or more groups. The setup is identical to the
1688 option umbrella, except for the fact that a rigid constraint is
1689 applied instead of a harmonic potential. Note that this type is
1690 not supported in combination with multiple time stepping.
1692 .. mdp-value:: constant-force
1694 Center of mass pulling using a linear potential and therefore a
1695 constant force. For this option there is no reference position
1696 and therefore the parameters :mdp:`pull-coord1-init` and
1697 :mdp:`pull-coord1-rate` are not used.
1699 .. mdp-value:: flat-bottom
1701 At distances above :mdp:`pull-coord1-init` a harmonic potential
1702 is applied, otherwise no potential is applied.
1704 .. mdp-value:: flat-bottom-high
1706 At distances below :mdp:`pull-coord1-init` a harmonic potential
1707 is applied, otherwise no potential is applied.
1709 .. mdp-value:: external-potential
1711 An external potential that needs to be provided by another
1714 .. mdp:: pull-coord1-potential-provider
1716 The name of the external module that provides the potential for
1717 the case where :mdp:`pull-coord1-type` is external-potential.
1719 .. mdp:: pull-coord1-geometry
1721 .. mdp-value:: distance
1723 Pull along the vector connecting the two groups. Components can
1724 be selected with :mdp:`pull-coord1-dim`.
1726 .. mdp-value:: direction
1728 Pull in the direction of :mdp:`pull-coord1-vec`.
1730 .. mdp-value:: direction-periodic
1732 As :mdp-value:`pull-coord1-geometry=direction`, but does not apply
1733 periodic box vector corrections to keep the distance within half
1734 the box length. This is (only) useful for pushing groups apart
1735 by more than half the box length by continuously changing the reference
1736 location using a pull rate. With this geometry the box should not be
1737 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1738 the pull force is not added to the virial.
1740 .. mdp-value:: direction-relative
1742 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1743 that points from the COM of a third to the COM of a fourth pull
1744 group. This means that 4 groups need to be supplied in
1745 :mdp:`pull-coord1-groups`. Note that the pull force will give
1746 rise to a torque on the pull vector, which is turn leads to
1747 forces perpendicular to the pull vector on the two groups
1748 defining the vector. If you want a pull group to move between
1749 the two groups defining the vector, simply use the union of
1750 these two groups as the reference group.
1752 .. mdp-value:: cylinder
1754 Designed for pulling with respect to a layer where the reference
1755 COM is given by a local cylindrical part of the reference group.
1756 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1757 the first of the two groups in :mdp:`pull-coord1-groups` a
1758 cylinder is selected around the axis going through the COM of
1759 the second group with direction :mdp:`pull-coord1-vec` with
1760 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1761 continously to zero as the radial distance goes from 0 to
1762 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1763 dependence gives rise to radial forces on both pull groups.
1764 Note that the radius should be smaller than half the box size.
1765 For tilted cylinders they should be even smaller than half the
1766 box size since the distance of an atom in the reference group
1767 from the COM of the pull group has both a radial and an axial
1768 component. This geometry is not supported with constraint
1771 .. mdp-value:: angle
1773 Pull along an angle defined by four groups. The angle is
1774 defined as the angle between two vectors: the vector connecting
1775 the COM of the first group to the COM of the second group and
1776 the vector connecting the COM of the third group to the COM of
1779 .. mdp-value:: angle-axis
1781 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1782 Thus, only the two groups that define the first vector need to be given.
1784 .. mdp-value:: dihedral
1786 Pull along a dihedral angle defined by six groups. These pairwise
1787 define three vectors: the vector connecting the COM of group 1
1788 to the COM of group 2, the COM of group 3 to the COM of group 4,
1789 and the COM of group 5 to the COM group 6. The dihedral angle is
1790 then defined as the angle between two planes: the plane spanned by the
1791 the two first vectors and the plane spanned the two last vectors.
1794 .. mdp:: pull-coord1-groups
1796 The group indices on which this pull coordinate will operate.
1797 The number of group indices required is geometry dependent.
1798 The first index can be 0, in which case an
1799 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1800 absolute reference the system is no longer translation invariant
1801 and one should think about what to do with the center of mass
1804 .. mdp:: pull-coord1-dim
1807 Selects the dimensions that this pull coordinate acts on and that
1808 are printed to the output files when
1809 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1810 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1811 components set to Y contribute to the distance. Thus setting this
1812 to Y Y N results in a distance in the x/y plane. With other
1813 geometries all dimensions with non-zero entries in
1814 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1815 dimensions only affect the output.
1817 .. mdp:: pull-coord1-origin
1820 The pull reference position for use with an absolute reference.
1822 .. mdp:: pull-coord1-vec
1825 The pull direction. :ref:`gmx grompp` normalizes the vector.
1827 .. mdp:: pull-coord1-start
1831 do not modify :mdp:`pull-coord1-init`
1835 add the COM distance of the starting conformation to
1836 :mdp:`pull-coord1-init`
1838 .. mdp:: pull-coord1-init
1841 The reference distance or reference angle at t=0.
1843 .. mdp:: pull-coord1-rate
1845 (0) [nm/ps] or [deg/ps]
1846 The rate of change of the reference position or reference angle.
1848 .. mdp:: pull-coord1-k
1850 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1851 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1852 The force constant. For umbrella pulling this is the harmonic force
1853 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1854 for angles). For constant force pulling this is the
1855 force constant of the linear potential, and thus the negative (!)
1856 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1857 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1858 Note that for angles the force constant is expressed in terms of radians
1859 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1861 .. mdp:: pull-coord1-kB
1863 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1864 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1865 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1866 :mdp:`free-energy` is turned on. The force constant is then (1 -
1867 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1869 AWH adaptive biasing
1870 ^^^^^^^^^^^^^^^^^^^^
1880 Adaptively bias a reaction coordinate using the AWH method and estimate
1881 the corresponding PMF. The PMF and other AWH data are written to energy
1882 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1883 the ``gmx awh`` tool. The AWH coordinate can be
1884 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1885 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1886 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1887 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1889 .. mdp:: awh-potential
1891 .. mdp-value:: convolved
1893 The applied biasing potential is the convolution of the bias function and a
1894 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1895 in a smooth potential function and force. The resolution of the potential is set
1896 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1898 .. mdp-value:: umbrella
1900 The potential bias is applied by controlling the position of an harmonic potential
1901 using Monte-Carlo sampling. The force constant is set with
1902 :mdp:`awh1-dim1-force-constant`. The umbrella location
1903 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1904 There are no advantages to using an umbrella.
1905 This option is mainly for comparison and testing purposes.
1907 .. mdp:: awh-share-multisim
1911 AWH will not share biases across simulations started with
1912 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1916 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1917 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1918 with the biases with the same :mdp:`awh1-share-group` value.
1919 The simulations should have the same AWH settings for sharing to make sense.
1920 :ref:`gmx mdrun` will check whether the simulations are technically
1921 compatible for sharing, but the user should check that bias sharing
1922 physically makes sense.
1926 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1927 where -1 indicates to generate a seed. Only used with
1928 :mdp-value:`awh-potential=umbrella`.
1933 Number of steps between printing AWH data to the energy file, should be
1934 a multiple of :mdp:`nstenergy`.
1936 .. mdp:: awh-nstsample
1939 Number of steps between sampling of the coordinate value. This sampling
1940 is the basis for updating the bias and estimating the PMF and other AWH observables.
1942 .. mdp:: awh-nsamples-update
1945 The number of coordinate samples used for each AWH update.
1946 The update interval in steps is :mdp:`awh-nstsample` times this value.
1951 The number of biases, each acting on its own coordinate.
1952 The following options should be specified
1953 for each bias although below only the options for bias number 1 is shown. Options for
1954 other bias indices are obtained by replacing '1' by the bias index.
1956 .. mdp:: awh1-error-init
1958 (10.0) [kJ mol\ :sup:`-1`]
1959 Estimated initial average error of the PMF for this bias. This value together with the
1960 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1961 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1963 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1964 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1965 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1966 then :mdp:`awh1-error-init` should reflect that knowledge.
1968 .. mdp:: awh1-growth
1970 .. mdp-value:: exp-linear
1972 Each bias keeps a reference weight histogram for the coordinate samples.
1973 Its size sets the magnitude of the bias function and free energy estimate updates
1974 (few samples corresponds to large updates and vice versa).
1975 Thus, its growth rate sets the maximum convergence rate.
1976 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1977 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1978 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1979 high free energy barriers have not yet been flattened by the bias.
1981 .. mdp-value:: linear
1983 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1984 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
1985 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
1987 .. mdp:: awh1-equilibrate-histogram
1991 Do not equilibrate histogram.
1995 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
1996 histogram of sampled weights is following the target distribution closely enough (specifically,
1997 at least 80% of the target region needs to have a local relative error of less than 20%). This
1998 option would typically only be used when :mdp:`awh1-share-group` > 0
1999 and the initial configurations poorly represent the target
2002 .. mdp:: awh1-target
2004 .. mdp-value:: constant
2006 The bias is tuned towards a constant (uniform) coordinate distribution
2007 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
2009 .. mdp-value:: cutoff
2011 Similar to :mdp-value:`awh1-target=constant`, but the target
2012 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
2013 where F is the free energy relative to the estimated global minimum.
2014 This provides a smooth switch of a flat target distribution in
2015 regions with free energy lower than the cut-off to a Boltzmann
2016 distribution in regions with free energy higher than the cut-off.
2018 .. mdp-value:: boltzmann
2020 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
2021 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
2022 would give the same coordinate distribution as sampling with a simulation temperature
2025 .. mdp-value:: local-boltzmann
2027 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
2028 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
2029 change of the bias only depends on the local sampling. This local convergence property is
2030 only compatible with :mdp-value:`awh1-growth=linear`, since for
2031 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
2033 .. mdp:: awh1-target-beta-scaling
2036 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
2037 it is the unitless beta scaling factor taking values in (0,1).
2039 .. mdp:: awh1-target-cutoff
2041 (0) [kJ mol\ :sup:`-1`]
2042 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2044 .. mdp:: awh1-user-data
2048 Initialize the PMF and target distribution with default values.
2052 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2053 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2054 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2055 The file name can be changed with the ``-awh`` option.
2056 The first :mdp:`awh1-ndim` columns of
2057 each input file should contain the coordinate values, such that each row defines a point in
2058 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value (in kT) for each point.
2059 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2060 be in the same column as written by :ref:`gmx awh`.
2062 .. mdp:: awh1-share-group
2066 Do not share the bias.
2068 .. mdp-value:: positive
2070 Share the bias and PMF estimates within and/or between simulations.
2071 Within a simulation, the bias will be shared between biases that have the
2072 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2073 With :mdp-value:`awh-share-multisim=yes` and
2074 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2075 Sharing may increase convergence initially, although the starting configurations
2076 can be critical, especially when sharing between many biases.
2077 Currently, positive group values should start at 1 and increase
2078 by 1 for each subsequent bias that is shared.
2083 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2084 The following options should be specified for each such dimension. Below only
2085 the options for dimension number 1 is shown. Options for other dimension indices are
2086 obtained by replacing '1' by the dimension index.
2088 .. mdp:: awh1-dim1-coord-provider
2092 The pull module is providing the reaction coordinate for this dimension.
2093 With multiple time-stepping, AWH and pull should be in the same MTS level.
2095 .. mdp-value:: fep-lambda
2097 The free energy lambda state is the reaction coordinate for this dimension.
2098 The lambda states to use are specified by :mdp:`fep-lambdas`, :mdp:`vdw-lambdas`,
2099 :mdp:`coul-lambdas` etc. This is not compatible with delta-lambda. It also requires
2100 calc-lambda-neighbors to be -1. With multiple time-stepping, AWH should
2101 be in the slow level.
2103 .. mdp:: awh1-dim1-coord-index
2106 Index of the pull coordinate defining this coordinate dimension.
2108 .. mdp:: awh1-dim1-force-constant
2110 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2111 Force constant for the (convolved) umbrella potential(s) along this
2112 coordinate dimension.
2114 .. mdp:: awh1-dim1-start
2117 Start value of the sampling interval along this dimension. The range of allowed
2118 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2119 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2120 is allowed. The interval will then wrap around from +period/2 to -period/2.
2121 For the direction geometry, the dimension is made periodic when
2122 the direction is along a box vector and covers more than 95%
2123 of the box length. Note that one should not apply pressure coupling
2124 along a periodic dimension.
2126 .. mdp:: awh1-dim1-end
2129 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2131 .. mdp:: awh1-dim1-diffusion
2133 (10\ :sup:`-5`) [nm\ :sup:`2`/ps], [rad\ :sup:`2`/ps] or [ps\ :sup:`-1`]
2134 Estimated diffusion constant for this coordinate dimension determining the initial
2135 biasing rate. This needs only be a rough estimate and should not critically
2136 affect the results unless it is set to something very low, leading to slow convergence,
2137 or very high, forcing the system far from equilibrium. Not setting this value
2138 explicitly generates a warning.
2140 .. mdp:: awh1-dim1-cover-diameter
2143 Diameter that needs to be sampled by a single simulation around a coordinate value
2144 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2145 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2146 across each coordinate value.
2147 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2148 (:mdp:`awh1-share-group`>0).
2149 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2150 for many sharing simulations does not guarantee transitions across free energy barriers.
2151 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2152 has independently sampled the whole interval.
2157 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2158 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2159 that can be used to achieve such a rotation.
2165 No enforced rotation will be applied. All enforced rotation options will
2166 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2171 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2172 under the :mdp:`rot-group0` option.
2174 .. mdp:: rot-ngroups
2177 Number of rotation groups.
2181 Name of rotation group 0 in the index file.
2186 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2187 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2188 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2193 Use mass weighted rotation group positions.
2198 Rotation vector, will get normalized.
2203 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2207 (0) [degree ps\ :sup:`-1`]
2208 Reference rotation rate of group 0.
2212 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2213 Force constant for group 0.
2215 .. mdp:: rot-slab-dist0
2218 Slab distance, if a flexible axis rotation type was chosen.
2220 .. mdp:: rot-min-gauss0
2223 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2224 (for the flexible axis potentials).
2228 (0.0001) [nm\ :sup:`2`]
2229 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2231 .. mdp:: rot-fit-method0
2234 Fitting method when determining the actual angle of a rotation group
2235 (can be one of ``rmsd``, ``norm``, or ``potential``).
2237 .. mdp:: rot-potfit-nsteps0
2240 For fit type ``potential``, the number of angular positions around the reference angle for which the
2241 rotation potential is evaluated.
2243 .. mdp:: rot-potfit-step0
2246 For fit type ``potential``, the distance in degrees between two angular positions.
2248 .. mdp:: rot-nstrout
2251 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2252 and the rotation potential energy.
2254 .. mdp:: rot-nstsout
2257 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2267 ignore distance restraint information in topology file
2269 .. mdp-value:: simple
2271 simple (per-molecule) distance restraints.
2273 .. mdp-value:: ensemble
2275 distance restraints over an ensemble of molecules in one
2276 simulation box. Normally, one would perform ensemble averaging
2277 over multiple simulations, using ``mdrun
2278 -multidir``. The environment
2279 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2280 within each ensemble (usually equal to the number of directories
2281 supplied to ``mdrun -multidir``).
2283 .. mdp:: disre-weighting
2285 .. mdp-value:: equal
2287 divide the restraint force equally over all atom pairs in the
2290 .. mdp-value:: conservative
2292 the forces are the derivative of the restraint potential, this
2293 results in an weighting of the atom pairs to the reciprocal
2294 seventh power of the displacement. The forces are conservative
2295 when :mdp:`disre-tau` is zero.
2297 .. mdp:: disre-mixed
2301 the violation used in the calculation of the restraint force is
2302 the time-averaged violation
2306 the violation used in the calculation of the restraint force is
2307 the square root of the product of the time-averaged violation
2308 and the instantaneous violation
2312 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2313 force constant for distance restraints, which is multiplied by a
2314 (possibly) different factor for each restraint given in the ``fac``
2315 column of the interaction in the topology file.
2320 time constant for distance restraints running average. A value of
2321 zero turns off time averaging.
2323 .. mdp:: nstdisreout
2326 period between steps when the running time-averaged and
2327 instantaneous distances of all atom pairs involved in restraints
2328 are written to the energy file (can make the energy file very
2335 ignore orientation restraint information in topology file
2339 use orientation restraints, ensemble averaging can be performed
2340 with ``mdrun -multidir``
2344 (0) [kJ mol\ :sup:`-1`]
2345 force constant for orientation restraints, which is multiplied by a
2346 (possibly) different weight factor for each restraint, can be set
2347 to zero to obtain the orientations from a free simulation
2352 time constant for orientation restraints running average. A value
2353 of zero turns off time averaging.
2355 .. mdp:: orire-fitgrp
2357 fit group for orientation restraining. This group of atoms is used
2358 to determine the rotation **R** of the system with respect to the
2359 reference orientation. The reference orientation is the starting
2360 conformation of the first subsystem. For a protein, backbone is a
2363 .. mdp:: nstorireout
2366 period between steps when the running time-averaged and
2367 instantaneous orientations for all restraints, and the molecular
2368 order tensor are written to the energy file (can make the energy
2372 Free energy calculations
2373 ^^^^^^^^^^^^^^^^^^^^^^^^
2375 .. mdp:: free-energy
2379 Only use topology A.
2383 Interpolate between topology A (lambda=0) to topology B
2384 (lambda=1) and write the derivative of the Hamiltonian with
2385 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2386 or the Hamiltonian differences with respect to other lambda
2387 values (as specified with foreign lambda) to the energy file
2388 and/or to ``dhdl.xvg``, where they can be processed by, for
2389 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2390 are interpolated linearly as described in the manual. When
2391 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2392 used for the LJ and Coulomb interactions.
2396 Turns on expanded ensemble simulation, where the alchemical state
2397 becomes a dynamic variable, allowing jumping between different
2398 Hamiltonians. See the expanded ensemble options for controlling how
2399 expanded ensemble simulations are performed. The different
2400 Hamiltonians used in expanded ensemble simulations are defined by
2401 the other free energy options.
2403 .. mdp:: init-lambda
2406 starting value for lambda (float). Generally, this should only be
2407 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2408 other cases, :mdp:`init-lambda-state` should be specified
2409 instead. Must be greater than or equal to 0.
2411 .. mdp:: delta-lambda
2414 increment per time step for lambda
2416 .. mdp:: init-lambda-state
2419 starting value for the lambda state (integer). Specifies which
2420 columm of the lambda vector (:mdp:`coul-lambdas`,
2421 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2422 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2423 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2424 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2425 the first column, and so on.
2427 .. mdp:: fep-lambdas
2430 Zero, one or more lambda values for which Delta H values will be
2431 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2432 steps. Values must be between 0 and 1. Free energy differences
2433 between different lambda values can then be determined with
2434 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2435 other -lambdas keywords because all components of the lambda vector
2436 that are not specified will use :mdp:`fep-lambdas` (including
2437 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2439 .. mdp:: coul-lambdas
2442 Zero, one or more lambda values for which Delta H values will be
2443 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2444 steps. Values must be between 0 and 1. Only the electrostatic
2445 interactions are controlled with this component of the lambda
2446 vector (and only if the lambda=0 and lambda=1 states have differing
2447 electrostatic interactions).
2449 .. mdp:: vdw-lambdas
2452 Zero, one or more lambda values for which Delta H values will be
2453 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2454 steps. Values must be between 0 and 1. Only the van der Waals
2455 interactions are controlled with this component of the lambda
2458 .. mdp:: bonded-lambdas
2461 Zero, one or more lambda values for which Delta H values will be
2462 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2463 steps. Values must be between 0 and 1. Only the bonded interactions
2464 are controlled with this component of the lambda vector.
2466 .. mdp:: restraint-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 restraint
2472 interactions: dihedral restraints, and the pull code restraints are
2473 controlled with this component of the lambda vector.
2475 .. mdp:: mass-lambdas
2478 Zero, one or more lambda values for which Delta H values will be
2479 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2480 steps. Values must be between 0 and 1. Only the particle masses are
2481 controlled with this component of the lambda vector.
2483 .. mdp:: temperature-lambdas
2486 Zero, one or more lambda values for which Delta H values will be
2487 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2488 steps. Values must be between 0 and 1. Only the temperatures
2489 controlled with this component of the lambda vector. Note that
2490 these lambdas should not be used for replica exchange, only for
2491 simulated tempering.
2493 .. mdp:: calc-lambda-neighbors
2496 Controls the number of lambda values for which Delta H values will
2497 be calculated and written out, if :mdp:`init-lambda-state` has
2498 been set. A positive value will limit the number of lambda points
2499 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2500 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2501 has a value of 2, energies for lambda points 3-7 will be calculated
2502 and writen out. A value of -1 means all lambda points will be
2503 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2504 1 is sufficient, while for MBAR -1 should be used.
2509 the soft-core alpha parameter, a value of 0 results in linear
2510 interpolation of the LJ and Coulomb interactions
2515 power 6 for the radial term in the soft-core equation.
2520 Whether to apply the soft-core free energy interaction
2521 transformation to the Columbic interaction of a molecule. Default
2522 is no, as it is generally more efficient to turn off the Coulomic
2523 interactions linearly before turning off the van der Waals
2524 interactions. Note that it is only taken into account when lambda
2525 states are used, not with :mdp:`couple-lambda0` /
2526 :mdp:`couple-lambda1`, and you can still turn off soft-core
2527 interactions by setting :mdp:`sc-alpha` to 0.
2532 the power for lambda in the soft-core function, only the values 1
2538 the soft-core sigma for particles which have a C6 or C12 parameter
2539 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2541 .. mdp:: couple-moltype
2543 Here one can supply a molecule type (as defined in the topology)
2544 for calculating solvation or coupling free energies. There is a
2545 special option ``system`` that couples all molecule types in the
2546 system. This can be useful for equilibrating a system starting from
2547 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2548 on. The Van der Waals interactions and/or charges in this molecule
2549 type can be turned on or off between lambda=0 and lambda=1,
2550 depending on the settings of :mdp:`couple-lambda0` and
2551 :mdp:`couple-lambda1`. If you want to decouple one of several
2552 copies of a molecule, you need to copy and rename the molecule
2553 definition in the topology.
2555 .. mdp:: couple-lambda0
2557 .. mdp-value:: vdw-q
2559 all interactions are on at lambda=0
2563 the charges are zero (no Coulomb interactions) at lambda=0
2567 the Van der Waals interactions are turned at lambda=0; soft-core
2568 interactions will be required to avoid singularities
2572 the Van der Waals interactions are turned off and the charges
2573 are zero at lambda=0; soft-core interactions will be required to
2574 avoid singularities.
2576 .. mdp:: couple-lambda1
2578 analogous to :mdp:`couple-lambda1`, but for lambda=1
2580 .. mdp:: couple-intramol
2584 All intra-molecular non-bonded interactions for moleculetype
2585 :mdp:`couple-moltype` are replaced by exclusions and explicit
2586 pair interactions. In this manner the decoupled state of the
2587 molecule corresponds to the proper vacuum state without
2588 periodicity effects.
2592 The intra-molecular Van der Waals and Coulomb interactions are
2593 also turned on/off. This can be useful for partitioning
2594 free-energies of relatively large molecules, where the
2595 intra-molecular non-bonded interactions might lead to
2596 kinetically trapped vacuum conformations. The 1-4 pair
2597 interactions are not turned off.
2602 the frequency for writing dH/dlambda and possibly Delta H to
2603 dhdl.xvg, 0 means no ouput, should be a multiple of
2604 :mdp:`nstcalcenergy`.
2606 .. mdp:: dhdl-derivatives
2610 If yes (the default), the derivatives of the Hamiltonian with
2611 respect to lambda at each :mdp:`nstdhdl` step are written
2612 out. These values are needed for interpolation of linear energy
2613 differences with :ref:`gmx bar` (although the same can also be
2614 achieved with the right foreign lambda setting, that may not be as
2615 flexible), or with thermodynamic integration
2617 .. mdp:: dhdl-print-energy
2621 Include either the total or the potential energy in the dhdl
2622 file. Options are 'no', 'potential', or 'total'. This information
2623 is needed for later free energy analysis if the states of interest
2624 are at different temperatures. If all states are at the same
2625 temperature, this information is not needed. 'potential' is useful
2626 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2627 file. When rerunning from an existing trajectory, the kinetic
2628 energy will often not be correct, and thus one must compute the
2629 residual free energy from the potential alone, with the kinetic
2630 energy component computed analytically.
2632 .. mdp:: separate-dhdl-file
2636 The free energy values that are calculated (as specified with
2637 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2638 written out to a separate file, with the default name
2639 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2644 The free energy values are written out to the energy output file
2645 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2646 steps), where they can be extracted with :ref:`gmx energy` or
2647 used directly with :ref:`gmx bar`.
2649 .. mdp:: dh-hist-size
2652 If nonzero, specifies the size of the histogram into which the
2653 Delta H values (specified with foreign lambda) and the derivative
2654 dH/dl values are binned, and written to ener.edr. This can be used
2655 to save disk space while calculating free energy differences. One
2656 histogram gets written for each foreign lambda and two for the
2657 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2658 histogram settings (too small size or too wide bins) can introduce
2659 errors. Do not use histograms unless you're certain you need it.
2661 .. mdp:: dh-hist-spacing
2664 Specifies the bin width of the histograms, in energy units. Used in
2665 conjunction with :mdp:`dh-hist-size`. This size limits the
2666 accuracy with which free energies can be calculated. Do not use
2667 histograms unless you're certain you need it.
2670 Expanded Ensemble calculations
2671 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2673 .. mdp:: nstexpanded
2675 The number of integration steps beween attempted moves changing the
2676 system Hamiltonian in expanded ensemble simulations. Must be a
2677 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2684 No Monte Carlo in state space is performed.
2686 .. mdp-value:: metropolis-transition
2688 Uses the Metropolis weights to update the expanded ensemble
2689 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2692 .. mdp-value:: barker-transition
2694 Uses the Barker transition critera to update the expanded
2695 ensemble weight of each state i, defined by exp(-beta_new
2696 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2698 .. mdp-value:: wang-landau
2700 Uses the Wang-Landau algorithm (in state space, not energy
2701 space) to update the expanded ensemble weights.
2703 .. mdp-value:: min-variance
2705 Uses the minimum variance updating method of Escobedo et al. to
2706 update the expanded ensemble weights. Weights will not be the
2707 free energies, but will rather emphasize states that need more
2708 sampling to give even uncertainty.
2710 .. mdp:: lmc-mc-move
2714 No Monte Carlo in state space is performed.
2716 .. mdp-value:: metropolis-transition
2718 Randomly chooses a new state up or down, then uses the
2719 Metropolis critera to decide whether to accept or reject:
2720 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2722 .. mdp-value:: barker-transition
2724 Randomly chooses a new state up or down, then uses the Barker
2725 transition critera to decide whether to accept or reject:
2726 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2728 .. mdp-value:: gibbs
2730 Uses the conditional weights of the state given the coordinate
2731 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2734 .. mdp-value:: metropolized-gibbs
2736 Uses the conditional weights of the state given the coordinate
2737 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2738 to move to, EXCLUDING the current state, then uses a rejection
2739 step to ensure detailed balance. Always more efficient that
2740 Gibbs, though only marginally so in many situations, such as
2741 when only the nearest neighbors have decent phase space
2747 random seed to use for Monte Carlo moves in state space. When
2748 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2750 .. mdp:: mc-temperature
2752 Temperature used for acceptance/rejection for Monte Carlo moves. If
2753 not specified, the temperature of the simulation specified in the
2754 first group of :mdp:`ref-t` is used.
2759 The cutoff for the histogram of state occupancies to be reset, and
2760 the free energy incrementor to be changed from delta to delta *
2761 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2762 each histogram) / (average number of samples at each
2763 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2764 histogram is only considered flat if all Nratio > 0.8 AND
2765 simultaneously all 1/Nratio > 0.8.
2770 Each time the histogram is considered flat, then the current value
2771 of the Wang-Landau incrementor for the free energies is multiplied
2772 by :mdp:`wl-scale`. Value must be between 0 and 1.
2774 .. mdp:: init-wl-delta
2777 The initial value of the Wang-Landau incrementor in kT. Some value
2778 near 1 kT is usually most efficient, though sometimes a value of
2779 2-3 in units of kT works better if the free energy differences are
2782 .. mdp:: wl-oneovert
2785 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2786 the large sample limit. There is significant evidence that the
2787 standard Wang-Landau algorithms in state space presented here
2788 result in free energies getting 'burned in' to incorrect values
2789 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2790 then when the incrementor becomes less than 1/N, where N is the
2791 mumber of samples collected (and thus proportional to the data
2792 collection time, hence '1 over t'), then the Wang-Lambda
2793 incrementor is set to 1/N, decreasing every step. Once this occurs,
2794 :mdp:`wl-ratio` is ignored, but the weights will still stop
2795 updating when the equilibration criteria set in
2796 :mdp:`lmc-weights-equil` is achieved.
2798 .. mdp:: lmc-repeats
2801 Controls the number of times that each Monte Carlo swap type is
2802 performed each iteration. In the limit of large numbers of Monte
2803 Carlo repeats, then all methods converge to Gibbs sampling. The
2804 value will generally not need to be different from 1.
2806 .. mdp:: lmc-gibbsdelta
2809 Limit Gibbs sampling to selected numbers of neighboring states. For
2810 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2811 sampling over all of the states that are defined. A positive value
2812 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2813 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2814 value of -1 means that all states are considered. For less than 100
2815 states, it is probably not that expensive to include all states.
2817 .. mdp:: lmc-forced-nstart
2820 Force initial state space sampling to generate weights. In order to
2821 come up with reasonable initial weights, this setting allows the
2822 simulation to drive from the initial to the final lambda state,
2823 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2824 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2825 sufficiently long (thousands of steps, perhaps), then the weights
2826 will be close to correct. However, in most cases, it is probably
2827 better to simply run the standard weight equilibration algorithms.
2829 .. mdp:: nst-transition-matrix
2832 Frequency of outputting the expanded ensemble transition matrix. A
2833 negative number means it will only be printed at the end of the
2836 .. mdp:: symmetrized-transition-matrix
2839 Whether to symmetrize the empirical transition matrix. In the
2840 infinite limit the matrix will be symmetric, but will diverge with
2841 statistical noise for short timescales. Forced symmetrization, by
2842 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2843 like the existence of (small magnitude) negative eigenvalues.
2845 .. mdp:: mininum-var-min
2848 The min-variance strategy (option of :mdp:`lmc-stats` is only
2849 valid for larger number of samples, and can get stuck if too few
2850 samples are used at each state. :mdp:`mininum-var-min` is the
2851 minimum number of samples that each state that are allowed before
2852 the min-variance strategy is activated if selected.
2854 .. mdp:: init-lambda-weights
2856 The initial weights (free energies) used for the expanded ensemble
2857 states. Default is a vector of zero weights. format is similar to
2858 the lambda vector settings in :mdp:`fep-lambdas`, except the
2859 weights can be any floating point number. Units are kT. Its length
2860 must match the lambda vector lengths.
2862 .. mdp:: lmc-weights-equil
2866 Expanded ensemble weights continue to be updated throughout the
2871 The input expanded ensemble weights are treated as equilibrated,
2872 and are not updated throughout the simulation.
2874 .. mdp-value:: wl-delta
2876 Expanded ensemble weight updating is stopped when the
2877 Wang-Landau incrementor falls below this value.
2879 .. mdp-value:: number-all-lambda
2881 Expanded ensemble weight updating is stopped when the number of
2882 samples at all of the lambda states is greater than this value.
2884 .. mdp-value:: number-steps
2886 Expanded ensemble weight updating is stopped when the number of
2887 steps is greater than the level specified by this value.
2889 .. mdp-value:: number-samples
2891 Expanded ensemble weight updating is stopped when the number of
2892 total samples across all lambda states is greater than the level
2893 specified by this value.
2895 .. mdp-value:: count-ratio
2897 Expanded ensemble weight updating is stopped when the ratio of
2898 samples at the least sampled lambda state and most sampled
2899 lambda state greater than this value.
2901 .. mdp:: simulated-tempering
2904 Turn simulated tempering on or off. Simulated tempering is
2905 implemented as expanded ensemble sampling with different
2906 temperatures instead of different Hamiltonians.
2908 .. mdp:: sim-temp-low
2911 Low temperature for simulated tempering.
2913 .. mdp:: sim-temp-high
2916 High temperature for simulated tempering.
2918 .. mdp:: simulated-tempering-scaling
2920 Controls the way that the temperatures at intermediate lambdas are
2921 calculated from the :mdp:`temperature-lambdas` part of the lambda
2924 .. mdp-value:: linear
2926 Linearly interpolates the temperatures using the values of
2927 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2928 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2929 a temperature of 350. A nonlinear set of temperatures can always
2930 be implemented with uneven spacing in lambda.
2932 .. mdp-value:: geometric
2934 Interpolates temperatures geometrically between
2935 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2936 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2937 :mdp:`sim-temp-low`) raised to the power of
2938 (i/(ntemps-1)). This should give roughly equal exchange for
2939 constant heat capacity, though of course things simulations that
2940 involve protein folding have very high heat capacity peaks.
2942 .. mdp-value:: exponential
2944 Interpolates temperatures exponentially between
2945 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2946 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2947 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2948 (i))-1)/(exp(1.0)-i)).
2956 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2957 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2958 specifies for which dimension(s) the freezing applies. To avoid
2959 spurious contributions to the virial and pressure due to large
2960 forces between completely frozen atoms you need to use energy group
2961 exclusions, this also saves computing time. Note that coordinates
2962 of frozen atoms are not scaled by pressure-coupling algorithms.
2966 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2967 specify ``Y`` or ``N`` for X, Y and Z and for each group (*e.g.*
2968 ``Y Y N N N N`` means that particles in the first group can move only in
2969 Z direction. The particles in the second group can move in any
2972 .. mdp:: cos-acceleration
2974 (0) [nm ps\ :sup:`-2`]
2975 the amplitude of the acceleration profile for calculating the
2976 viscosity. The acceleration is in the X-direction and the magnitude
2977 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2978 added to the energy file: the amplitude of the velocity profile and
2983 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
2984 The velocities of deformation for the box elements: a(x) b(y) c(z)
2985 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2986 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2987 elements are corrected for periodicity. The coordinates are
2988 transformed accordingly. Frozen degrees of freedom are (purposely)
2989 also transformed. The time ts is set to t at the first step and at
2990 steps at which x and v are written to trajectory to ensure exact
2991 restarts. Deformation can be used together with semiisotropic or
2992 anisotropic pressure coupling when the appropriate
2993 compressibilities are set to zero. The diagonal elements can be
2994 used to strain a solid. The off-diagonal elements can be used to
2995 shear a solid or a liquid.
3001 .. mdp:: electric-field-x
3002 .. mdp:: electric-field-y
3003 .. mdp:: electric-field-z
3005 Here you can specify an electric field that optionally can be
3006 alternating and pulsed. The general expression for the field
3007 has the form of a gaussian laser pulse:
3009 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
3011 For example, the four parameters for direction x are set in the
3012 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
3013 and ``electric-field-z``) like
3015 ``electric-field-x = E0 omega t0 sigma``
3017 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
3019 In the special case that ``sigma = 0``, the exponential term is omitted
3020 and only the cosine term is used. If also ``omega = 0`` a static
3021 electric field is applied.
3023 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
3026 Mixed quantum/classical molecular dynamics
3027 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3031 groups to be descibed at the QM level for MiMiC QM/MM
3037 QM/MM is no longer supported via these .mdp options. For MiMic, use no here.
3039 Computational Electrophysiology
3040 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3041 Use these options to switch on and control ion/water position exchanges in "Computational
3042 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3048 Do not enable ion/water position exchanges.
3050 .. mdp-value:: X ; Y ; Z
3052 Allow for ion/water position exchanges along the chosen direction.
3053 In a typical setup with the membranes parallel to the x-y plane,
3054 ion/water pairs need to be exchanged in Z direction to sustain the
3055 requested ion concentrations in the compartments.
3057 .. mdp:: swap-frequency
3059 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3060 per compartment are determined and exchanges made if necessary.
3061 Normally it is not necessary to check at every time step.
3062 For typical Computational Electrophysiology setups, a value of about 100 is
3063 sufficient and yields a negligible performance impact.
3065 .. mdp:: split-group0
3067 Name of the index group of the membrane-embedded part of channel #0.
3068 The center of mass of these atoms defines one of the compartment boundaries
3069 and should be chosen such that it is near the center of the membrane.
3071 .. mdp:: split-group1
3073 Channel #1 defines the position of the other compartment boundary.
3075 .. mdp:: massw-split0
3077 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3081 Use the geometrical center.
3085 Use the center of mass.
3087 .. mdp:: massw-split1
3089 (no) As above, but for split-group #1.
3091 .. mdp:: solvent-group
3093 Name of the index group of solvent molecules.
3095 .. mdp:: coupl-steps
3097 (10) Average the number of ions per compartment over these many swap attempt steps.
3098 This can be used to prevent that ions near a compartment boundary
3099 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3103 (1) The number of different ion types to be controlled. These are during the
3104 simulation exchanged with solvent molecules to reach the desired reference numbers.
3106 .. mdp:: iontype0-name
3108 Name of the first ion type.
3110 .. mdp:: iontype0-in-A
3112 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3113 The default value of -1 means: use the number of ions as found in time step 0
3116 .. mdp:: iontype0-in-B
3118 (-1) Reference number of ions of type 0 for compartment B.
3120 .. mdp:: bulk-offsetA
3122 (0.0) Offset of the first swap layer from the compartment A midplane.
3123 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3124 at maximum distance (= bulk concentration) to the split group layers. However,
3125 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3126 towards one of the compartment-partitioning layers (at +/- 1.0).
3128 .. mdp:: bulk-offsetB
3130 (0.0) Offset of the other swap layer from the compartment B midplane.
3135 (\1) Only swap ions if threshold difference to requested count is reached.
3139 (2.0) [nm] Radius of the split cylinder #0.
3140 Two split cylinders (mimicking the channel pores) can optionally be defined
3141 relative to the center of the split group. With the help of these cylinders
3142 it can be counted which ions have passed which channel. The split cylinder
3143 definition has no impact on whether or not ion/water swaps are done.
3147 (1.0) [nm] Upper extension of the split cylinder #0.
3151 (1.0) [nm] Lower extension of the split cylinder #0.
3155 (2.0) [nm] Radius of the split cylinder #1.
3159 (1.0) [nm] Upper extension of the split cylinder #1.
3163 (1.0) [nm] Lower extension of the split cylinder #1.
3165 Density-guided simulations
3166 ^^^^^^^^^^^^^^^^^^^^^^^^^^
3168 These options enable and control the calculation and application of additional
3169 forces that are derived from three-dimensional densities, e.g., from cryo
3170 electron-microscopy experiments. (See the `reference manual`_ for details)
3172 .. mdp:: density-guided-simulation-active
3174 (no) Activate density-guided simulations.
3176 .. mdp:: density-guided-simulation-group
3178 (protein) The atoms that are subject to the forces from the density-guided
3179 simulation and contribute to the simulated density.
3181 .. mdp:: density-guided-simulation-similarity-measure
3183 (inner-product) Similarity measure between the density that is calculated
3184 from the atom positions and the reference density.
3186 .. mdp-value:: inner-product
3188 Takes the sum of the product of reference density and simulated density
3191 .. mdp-value:: relative-entropy
3193 Uses the negative relative entropy (or Kullback-Leibler divergence)
3194 between reference density and simulated density as similarity measure.
3195 Negative density values are ignored.
3197 .. mdp-value:: cross-correlation
3199 Uses the Pearson correlation coefficient between reference density and
3200 simulated density as similarity measure.
3202 .. mdp:: density-guided-simulation-atom-spreading-weight
3204 (unity) Determines the multiplication factor for the Gaussian kernel when
3205 spreading atoms on the grid.
3207 .. mdp-value:: unity
3209 Every atom in the density fitting group is assigned the same unit factor.
3213 Atoms contribute to the simulated density proportional to their mass.
3215 .. mdp-value:: charge
3217 Atoms contribute to the simulated density proportional to their charge.
3219 .. mdp:: density-guided-simulation-force-constant
3221 (1e+09) [kJ mol\ :sup:`-1`] The scaling factor for density-guided simulation
3222 forces. May also be negative.
3224 .. mdp:: density-guided-simulation-gaussian-transform-spreading-width
3226 (0.2) [nm] The Gaussian RMS width for the spread kernel for the simulated
3229 .. mdp:: density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width
3231 (4) The range after which the gaussian is cut off in multiples of the Gaussian
3232 RMS width described above.
3234 .. mdp:: density-guided-simulation-reference-density-filename
3236 (reference.mrc) Reference density file name using an absolute path or a path
3237 relative to the to the folder from which :ref:`gmx mdrun` is called.
3239 .. mdp:: density-guided-simulation-nst
3241 (1) Interval in steps at which the density fitting forces are evaluated
3242 and applied. The forces are scaled by this number when applied (See the
3243 `reference manual`_ for details).
3245 .. mdp:: density-guided-simulation-normalize-densities
3247 (true) Normalize the sum of density voxel values to one for the reference
3248 density as well as the simulated density.
3250 .. mdp:: density-guided-simulation-adaptive-force-scaling
3252 (false) Adapt the force constant to ensure a steady increase in similarity
3253 between simulated and reference density.
3257 Do not use adaptive force scaling.
3261 Use adaptive force scaling.
3263 .. mdp:: density-guided-simulation-adaptive-force-scaling-time-constant
3265 (4) [ps] Couple force constant to increase in similarity with reference density
3266 with this time constant. Larger times result in looser coupling.
3268 .. mdp:: density-guided-simulation-shift-vector
3270 (0,0,0) [nm] Add this vector to all atoms in the
3271 density-guided-simulation-group before calculating forces and energies for
3272 density-guided-simulations. Affects only the density-guided-simulation forces
3273 and energies. Corresponds to a shift of the input density in the opposite
3274 direction by (-1) * density-guided-simulation-shift-vector.
3276 .. mdp:: density-guided-simulation-transformation-matrix
3278 (1,0,0,0,1,0,0,0,1) Multiply all atoms with this matrix in the
3279 density-guided-simulation-group before calculating forces and energies for
3280 density-guided-simulations. Affects only the density-guided-simulation forces
3281 and energies. Corresponds to a transformation of the input density by the
3282 inverse of this matrix. The matrix is given in row-major order.
3283 This option allows, e.g., rotation of the density-guided atom group around the
3284 z-axis by :math:`\theta` degress by using following input:
3285 :math:`(\cos \theta , -\sin \theta , 0 , \sin \theta , \cos \theta , 0 , 0 , 0 , 1)` .
3287 User defined thingies
3288 ^^^^^^^^^^^^^^^^^^^^^
3292 .. mdp:: userint1 (0)
3293 .. mdp:: userint2 (0)
3294 .. mdp:: userint3 (0)
3295 .. mdp:: userint4 (0)
3296 .. mdp:: userreal1 (0)
3297 .. mdp:: userreal2 (0)
3298 .. mdp:: userreal3 (0)
3299 .. mdp:: userreal4 (0)
3301 These you can use if you modify code. You can pass integers and
3302 reals and groups to your subroutine. Check the inputrec definition
3303 in ``src/gromacs/mdtypes/inputrec.h``
3308 These features have been removed from |Gromacs|, but so that old
3309 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3310 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3311 fatal error if this is set.
3317 .. mdp:: implicit-solvent
3321 .. _reference manual: gmx-manual-parent-dir_