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.
236 .. mdp-value:: Linear
238 Remove center of mass translational velocity
240 .. mdp-value:: Angular
242 Remove center of mass translational and rotational velocity
244 .. mdp-value:: Linear-acceleration-correction
246 Remove center of mass translational velocity. Correct the center of
247 mass position assuming linear acceleration over :mdp:`nstcomm` steps.
248 This is useful for cases where an acceleration is expected on the
249 center of mass which is nearly constant over :mdp:`nstcomm` steps.
250 This can occur for example when pulling on a group using an absolute
255 No restriction on the center of mass motion
260 frequency for center of mass motion removal
264 group(s) for center of mass motion removal, default is the whole
273 (0) [amu ps\ :sup:`-1`]
274 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
275 the friction coefficient for each particle is calculated as mass/
281 used to initialize random generator for thermal noise for
282 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
283 a pseudo random seed is used. When running BD or SD on multiple
284 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
285 the processor number.
293 (10.0) [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
294 the minimization is converged when the maximum force is smaller
305 frequency of performing 1 steepest descent step while doing
306 conjugate gradient energy minimization.
311 Number of correction steps to use for L-BFGS minimization. A higher
312 number is (at least theoretically) more accurate, but slower.
315 Shell Molecular Dynamics
316 ^^^^^^^^^^^^^^^^^^^^^^^^
318 When shells or flexible constraints are present in the system the
319 positions of the shells and the lengths of the flexible constraints
320 are optimized at every time step until either the RMS force on the
321 shells and constraints is less than :mdp:`emtol`, or a maximum number
322 of iterations :mdp:`niter` has been reached. Minimization is converged
323 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
324 value should be 1.0 at most.
329 maximum number of iterations for optimizing the shell positions and
330 the flexible constraints.
335 the step size for optimizing the flexible constraints. Should be
336 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
337 particles in a flexible constraint and d2V/dq2 is the second
338 derivative of the potential in the constraint direction. Hopefully
339 this number does not differ too much between the flexible
340 constraints, as the number of iterations and thus the runtime is
341 very sensitive to fcstep. Try several values!
344 Test particle insertion
345 ^^^^^^^^^^^^^^^^^^^^^^^
350 the test particle insertion radius, see integrators
351 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
360 number of steps that elapse between writing coordinates to the output
361 trajectory file (:ref:`trr`), the last coordinates are always written
362 unless 0, which means coordinates are not written into the trajectory
368 number of steps that elapse between writing velocities to the output
369 trajectory file (:ref:`trr`), the last velocities are always written
370 unless 0, which means velocities are not written into the trajectory
376 number of steps that elapse between writing forces to the output
377 trajectory file (:ref:`trr`), the last forces are always written,
378 unless 0, which means forces are not written into the trajectory
384 number of steps that elapse between writing energies to the log
385 file, the last energies are always written.
387 .. mdp:: nstcalcenergy
390 number of steps that elapse between calculating the energies, 0 is
391 never. This option is only relevant with dynamics. This option affects the
392 performance in parallel simulations, because calculating energies
393 requires global communication between all processes which can
394 become a bottleneck at high parallelization.
399 number of steps that elapse between writing energies to energy file,
400 the last energies are always written, should be a multiple of
401 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
402 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
403 energy file, so :ref:`gmx energy` can report exact energy averages
404 and fluctuations also when :mdp:`nstenergy` > 1
406 .. mdp:: nstxout-compressed
409 number of steps that elapse between writing position coordinates
410 using lossy compression (:ref:`xtc` file), 0 for not writing
411 compressed coordinates output.
413 .. mdp:: compressed-x-precision
416 precision with which to write to the compressed trajectory file
418 .. mdp:: compressed-x-grps
420 group(s) to write to the compressed trajectory file, by default the
421 whole system is written (if :mdp:`nstxout-compressed` > 0)
425 group(s) for which to write to write short-ranged non-bonded
426 potential energies to the energy file (not supported on GPUs)
432 .. mdp:: cutoff-scheme
434 .. mdp-value:: Verlet
436 Generate a pair list with buffering. The buffer size is
437 automatically set based on :mdp:`verlet-buffer-tolerance`,
438 unless this is set to -1, in which case :mdp:`rlist` will be
443 Generate a pair list for groups of atoms, corresponding
444 to the charge groups in the topology. This option is no longer
453 Frequency to update the neighbor list. When dynamics and
454 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
455 a minimum value and :ref:`gmx mdrun` might increase it, unless
456 it is set to 1. With parallel simulations and/or non-bonded
457 force calculation on the GPU, a value of 20 or 40 often gives
458 the best performance.
462 The neighbor list is only constructed once and never
463 updated. This is mainly useful for vacuum simulations in which
464 all particles see each other. But vacuum simulations are
465 (temporarily) not supported.
475 Use periodic boundary conditions in all directions.
479 Use no periodic boundary conditions, ignore the box. To simulate
480 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
481 best performance without cut-offs on a single MPI rank, set
482 :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`.
486 Use periodic boundary conditions in x and y directions
487 only. This works only with :mdp-value:`ns-type=grid` and can be used
488 in combination with walls_. Without walls or with only one wall
489 the system size is infinite in the z direction. Therefore
490 pressure coupling or Ewald summation methods can not be
491 used. These disadvantages do not apply when two walls are used.
493 .. mdp:: periodic-molecules
497 molecules are finite, fast molecular PBC can be used
501 for systems with molecules that couple to themselves through the
502 periodic boundary conditions, this requires a slower PBC
503 algorithm and molecules are not made whole in the output
505 .. mdp:: verlet-buffer-tolerance
507 (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
509 Used when performing a simulation with dynamics. This sets
510 the maximum allowed error for pair interactions per particle caused
511 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
512 :mdp:`nstlist` and the Verlet buffer size are fixed (for
513 performance reasons), particle pairs not in the pair list can
514 occasionally get within the cut-off distance during
515 :mdp:`nstlist` -1 steps. This causes very small jumps in the
516 energy. In a constant-temperature ensemble, these very small energy
517 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
518 estimate assumes a homogeneous particle distribution, hence the
519 errors might be slightly underestimated for multi-phase
520 systems. (See the `reference manual`_ for details). For longer
521 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
522 overestimated, because the interactions between particles are
523 ignored. Combined with cancellation of errors, the actual drift of
524 the total energy is usually one to two orders of magnitude
525 smaller. Note that the generated buffer size takes into account
526 that the |Gromacs| pair-list setup leads to a reduction in the
527 drift by a factor 10, compared to a simple particle-pair based
528 list. Without dynamics (energy minimization etc.), the buffer is 5%
529 of the cut-off. For NVE simulations the initial temperature is
530 used, unless this is zero, in which case a buffer of 10% is
531 used. For NVE simulations the tolerance usually needs to be lowered
532 to achieve proper energy conservation on the nanosecond time
533 scale. To override the automated buffer setting, use
534 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
539 Cut-off distance for the short-range neighbor list. With dynamics,
540 this is by default set by the :mdp:`verlet-buffer-tolerance` option
541 and the value of :mdp:`rlist` is ignored. Without dynamics, this
542 is by default set to the maximum cut-off plus 5% buffer, except
543 for test particle insertion, where the buffer is managed exactly
544 and automatically. For NVE simulations, where the automated
545 setting is not possible, the advised procedure is to run :ref:`gmx grompp`
546 with an NVT setup with the expected temperature and copy the resulting
547 value of :mdp:`rlist` to the NVE setup.
555 .. mdp-value:: Cut-off
557 Plain cut-off with pair list radius :mdp:`rlist` and
558 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
563 Classical Ewald sum electrostatics. The real-space cut-off
564 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
565 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
566 of wave vectors used in reciprocal space is controlled by
567 :mdp:`fourierspacing`. The relative accuracy of
568 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
570 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
571 large systems. It is included mainly for reference - in most
572 cases PME will perform much better.
576 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
577 space is similar to the Ewald sum, while the reciprocal part is
578 performed with FFTs. Grid dimensions are controlled with
579 :mdp:`fourierspacing` and the interpolation order with
580 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
581 interpolation the electrostatic forces have an accuracy of
582 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
583 this you might try 0.15 nm. When running in parallel the
584 interpolation parallelizes better than the FFT, so try
585 decreasing grid dimensions while increasing interpolation.
587 .. mdp-value:: P3M-AD
589 Particle-Particle Particle-Mesh algorithm with analytical
590 derivative for for long range electrostatic interactions. The
591 method and code is identical to SPME, except that the influence
592 function is optimized for the grid. This gives a slight increase
595 .. mdp-value:: Reaction-Field
597 Reaction field electrostatics with Coulomb cut-off
598 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
599 dielectric constant beyond the cut-off is
600 :mdp:`epsilon-rf`. The dielectric constant can be set to
601 infinity by setting :mdp:`epsilon-rf` =0.
605 Currently unsupported.
606 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
607 with user-defined potential functions for repulsion, dispersion
608 and Coulomb. When pair interactions are present, :ref:`gmx
609 mdrun` also expects to find a file ``tablep.xvg`` for the pair
610 interactions. When the same interactions should be used for
611 non-bonded and pair interactions the user can specify the same
612 file name for both table files. These files should contain 7
613 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
614 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
615 function, ``g(x)`` the dispersion function and ``h(x)`` the
616 repulsion function. When :mdp:`vdwtype` is not set to User the
617 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
618 the non-bonded interactions ``x`` values should run from 0 to
619 the largest cut-off distance + :mdp:`table-extension` and
620 should be uniformly spaced. For the pair interactions the table
621 length in the file will be used. The optimal spacing, which is
622 used for non-user tables, is ``0.002 nm`` when you run in mixed
623 precision or ``0.0005 nm`` when you run in double precision. The
624 function value at ``x=0`` is not important. More information is
625 in the printed manual.
627 .. mdp-value:: PME-Switch
629 Currently unsupported.
630 A combination of PME and a switch function for the direct-space
631 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
634 .. mdp-value:: PME-User
636 Currently unsupported.
637 A combination of PME and user tables (see
638 above). :mdp:`rcoulomb` is allowed to be smaller than
639 :mdp:`rlist`. The PME mesh contribution is subtracted from the
640 user table by :ref:`gmx mdrun`. Because of this subtraction the
641 user tables should contain about 10 decimal places.
643 .. mdp-value:: PME-User-Switch
645 Currently unsupported.
646 A combination of PME-User and a switching function (see
647 above). The switching function is applied to final
648 particle-particle interaction, *i.e.* both to the user supplied
649 function and the PME Mesh correction part.
651 .. mdp:: coulomb-modifier
653 .. mdp-value:: Potential-shift
655 Shift the Coulomb potential by a constant such that it is zero
656 at the cut-off. This makes the potential the integral of the
657 force. Note that this does not affect the forces or the
662 Use an unmodified Coulomb potential. This can be useful
663 when comparing energies with those computed with other software.
665 .. mdp:: rcoulomb-switch
668 where to start switching the Coulomb potential, only relevant
669 when force or potential switching is used
674 The distance for the Coulomb cut-off. Note that with PME this value
675 can be increased by the PME tuning in :ref:`gmx mdrun` along with
676 the PME grid spacing.
681 The relative dielectric constant. A value of 0 means infinity.
686 The relative dielectric constant of the reaction field. This
687 is only used with reaction-field electrostatics. A value of 0
696 .. mdp-value:: Cut-off
698 Plain cut-off with pair list radius :mdp:`rlist` and VdW
699 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
703 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
704 grid dimensions are controlled with :mdp:`fourierspacing` in
705 the same way as for electrostatics, and the interpolation order
706 is controlled with :mdp:`pme-order`. The relative accuracy of
707 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
708 and the specific combination rules that are to be used by the
709 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
713 This functionality is deprecated and replaced by using
714 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
715 The LJ (not Buckingham) potential is decreased over the whole range and
716 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
719 .. mdp-value:: Switch
721 This functionality is deprecated and replaced by using
722 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
723 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
724 which it is switched off to reach zero at :mdp:`rvdw`. Both the
725 potential and force functions are continuously smooth, but be
726 aware that all switch functions will give rise to a bulge
727 (increase) in the force (since we are switching the
732 Currently unsupported.
733 See user for :mdp:`coulombtype`. The function value at zero is
734 not important. When you want to use LJ correction, make sure
735 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
736 function. When :mdp:`coulombtype` is not set to User the values
737 for the ``f`` and ``-f'`` columns are ignored.
739 .. mdp:: vdw-modifier
741 .. mdp-value:: Potential-shift
743 Shift the Van der Waals potential by a constant such that it is
744 zero at the cut-off. This makes the potential the integral of
745 the force. Note that this does not affect the forces or the
750 Use an unmodified Van der Waals potential. This can be useful
751 when comparing energies with those computed with other software.
753 .. mdp-value:: Force-switch
755 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
756 and :mdp:`rvdw`. This shifts the potential shift over the whole
757 range and switches it to zero at the cut-off. Note that this is
758 more expensive to calculate than a plain cut-off and it is not
759 required for energy conservation, since Potential-shift
760 conserves energy just as well.
762 .. mdp-value:: Potential-switch
764 Smoothly switches the potential to zero between
765 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
766 articifically large forces in the switching region and is much
767 more expensive to calculate. This option should only be used if
768 the force field you are using requires this.
773 where to start switching the LJ force and possibly the potential,
774 only relevant when force or potential switching is used
779 distance for the LJ or Buckingham cut-off
785 don't apply any correction
787 .. mdp-value:: EnerPres
789 apply long range dispersion corrections for Energy and Pressure
793 apply long range dispersion corrections for Energy only
799 .. mdp:: table-extension
802 Extension of the non-bonded potential lookup tables beyond the
803 largest cut-off distance. With actual non-bonded interactions
804 the tables are never accessed beyond the cut-off. But a longer
805 table length might be needed for the 1-4 interactions, which
806 are always tabulated irrespective of the use of tables for
807 the non-bonded interactions.
809 .. mdp:: energygrp-table
811 Currently unsupported.
812 When user tables are used for electrostatics and/or VdW, here one
813 can give pairs of energy groups for which seperate user tables
814 should be used. The two energy groups will be appended to the table
815 file name, in order of their definition in :mdp:`energygrps`,
816 seperated by underscores. For example, if ``energygrps = Na Cl
817 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
818 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
819 normal ``table.xvg`` which will be used for all other energy group
826 .. mdp:: fourierspacing
829 For ordinary Ewald, the ratio of the box dimensions and the spacing
830 determines a lower bound for the number of wave vectors to use in
831 each (signed) direction. For PME and P3M, that ratio determines a
832 lower bound for the number of Fourier-space grid points that will
833 be used along that axis. In all cases, the number for each
834 direction can be overridden by entering a non-zero value for that
835 :mdp:`fourier-nx` direction. For optimizing the relative load of
836 the particle-particle interactions and the mesh part of PME, it is
837 useful to know that the accuracy of the electrostatics remains
838 nearly constant when the Coulomb cut-off and the PME grid spacing
839 are scaled by the same factor. Note that this spacing can be scaled
840 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
847 Highest magnitude of wave vectors in reciprocal space when using Ewald.
848 Grid size when using PME or P3M. These values override
849 :mdp:`fourierspacing` per direction. The best choice is powers of
850 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
851 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
857 Interpolation order for PME. 4 equals cubic interpolation. You
858 might try 6/8/10 when running in parallel and simultaneously
859 decrease grid dimension.
864 The relative strength of the Ewald-shifted direct potential at
865 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
866 will give a more accurate direct sum, but then you need more wave
867 vectors for the reciprocal sum.
869 .. mdp:: ewald-rtol-lj
872 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
873 to control the relative strength of the dispersion potential at
874 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
875 electrostatic potential.
877 .. mdp:: lj-pme-comb-rule
880 The combination rules used to combine VdW-parameters in the
881 reciprocal part of LJ-PME. Geometric rules are much faster than
882 Lorentz-Berthelot and usually the recommended choice, even when the
883 rest of the force field uses the Lorentz-Berthelot rules.
885 .. mdp-value:: Geometric
887 Apply geometric combination rules
889 .. mdp-value:: Lorentz-Berthelot
891 Apply Lorentz-Berthelot combination rules
893 .. mdp:: ewald-geometry
897 The Ewald sum is performed in all three dimensions.
901 The reciprocal sum is still performed in 3D, but a force and
902 potential correction applied in the ``z`` dimension to produce a
903 pseudo-2D summation. If your system has a slab geometry in the
904 ``x-y`` plane you can try to increase the ``z``-dimension of the box
905 (a box height of 3 times the slab height is usually ok) and use
908 .. mdp:: epsilon-surface
911 This controls the dipole correction to the Ewald summation in
912 3D. The default value of zero means it is turned off. Turn it on by
913 setting it to the value of the relative permittivity of the
914 imaginary surface around your infinite system. Be careful - you
915 shouldn't use this if you have free mobile charges in your
916 system. This value does not affect the slab 3DC variant of the long
927 No temperature coupling.
929 .. mdp-value:: berendsen
931 Temperature coupling with a Berendsen thermostat to a bath with
932 temperature :mdp:`ref-t`, with time constant
933 :mdp:`tau-t`. Several groups can be coupled separately, these
934 are specified in the :mdp:`tc-grps` field separated by spaces.
936 .. mdp-value:: nose-hoover
938 Temperature coupling using a Nose-Hoover extended ensemble. The
939 reference temperature and coupling groups are selected as above,
940 but in this case :mdp:`tau-t` controls the period of the
941 temperature fluctuations at equilibrium, which is slightly
942 different from a relaxation time. For NVT simulations the
943 conserved energy quantity is written to the energy and log files.
945 .. mdp-value:: andersen
947 Temperature coupling by randomizing a fraction of the particle velocities
948 at each timestep. Reference temperature and coupling groups are
949 selected as above. :mdp:`tau-t` is the average time between
950 randomization of each molecule. Inhibits particle dynamics
951 somewhat, but little or no ergodicity issues. Currently only
952 implemented with velocity Verlet, and not implemented with
955 .. mdp-value:: andersen-massive
957 Temperature coupling by randomizing velocities of all particles at
958 infrequent timesteps. Reference temperature and coupling groups are
959 selected as above. :mdp:`tau-t` is the time between
960 randomization of all molecules. Inhibits particle dynamics
961 somewhat, but little or no ergodicity issues. Currently only
962 implemented with velocity Verlet.
964 .. mdp-value:: v-rescale
966 Temperature coupling using velocity rescaling with a stochastic
967 term (JCP 126, 014101). This thermostat is similar to Berendsen
968 coupling, with the same scaling using :mdp:`tau-t`, but the
969 stochastic term ensures that a proper canonical ensemble is
970 generated. The random seed is set with :mdp:`ld-seed`. This
971 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
972 simulations the conserved energy quantity is written to the
978 The frequency for coupling the temperature. The default value of -1
979 sets :mdp:`nsttcouple` equal to 10, or fewer steps if required
980 for accurate integration. Note that the default value is not 1
981 because additional computation and communication is required for
982 obtaining the kinetic energy. For velocity
983 Verlet integrators :mdp:`nsttcouple` is set to 1.
985 .. mdp:: nh-chain-length
988 The number of chained Nose-Hoover thermostats for velocity Verlet
989 integrators, the leap-frog :mdp-value:`integrator=md` integrator
990 only supports 1. Data for the NH chain variables is not printed
991 to the :ref:`edr` file by default, but can be turned on with the
992 :mdp:`print-nose-hoover-chain-variables` option.
994 .. mdp:: print-nose-hoover-chain-variables
998 Do not store Nose-Hoover chain variables in the energy file.
1002 Store all positions and velocities of the Nose-Hoover chain
1007 groups to couple to separate temperature baths
1012 time constant for coupling (one for each group in
1013 :mdp:`tc-grps`), -1 means no temperature coupling
1018 reference temperature for coupling (one for each group in
1029 No pressure coupling. This means a fixed box size.
1031 .. mdp-value:: Berendsen
1033 Exponential relaxation pressure coupling with time constant
1034 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1035 argued that this does not yield a correct thermodynamic
1036 ensemble, but it is the most efficient way to scale a box at the
1039 .. mdp-value:: C-rescale
1041 Exponential relaxation pressure coupling with time constant
1042 :mdp:`tau-p`, including a stochastic term to enforce correct
1043 volume fluctuations. The box is scaled every :mdp:`nstpcouple`
1044 steps. It can be used for both equilibration and production.
1046 .. mdp-value:: Parrinello-Rahman
1048 Extended-ensemble pressure coupling where the box vectors are
1049 subject to an equation of motion. The equation of motion for the
1050 atoms is coupled to this. No instantaneous scaling takes
1051 place. As for Nose-Hoover temperature coupling the time constant
1052 :mdp:`tau-p` is the period of pressure fluctuations at
1053 equilibrium. This is probably a better method when you want to
1054 apply pressure scaling during data collection, but beware that
1055 you can get very large oscillations if you are starting from a
1056 different pressure. For simulations where the exact fluctations
1057 of the NPT ensemble are important, or if the pressure coupling
1058 time is very short it may not be appropriate, as the previous
1059 time step pressure is used in some steps of the |Gromacs|
1060 implementation for the current time step pressure.
1064 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1065 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1066 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1067 time constant :mdp:`tau-p` is the period of pressure
1068 fluctuations at equilibrium. This is probably a better method
1069 when you want to apply pressure scaling during data collection,
1070 but beware that you can get very large oscillations if you are
1071 starting from a different pressure. Currently (as of version
1072 5.1), it only supports isotropic scaling, and only works without
1077 Specifies the kind of isotropy of the pressure coupling used. Each
1078 kind takes one or more values for :mdp:`compressibility` and
1079 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1081 .. mdp-value:: isotropic
1083 Isotropic pressure coupling with time constant
1084 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1085 :mdp:`ref-p` is required.
1087 .. mdp-value:: semiisotropic
1089 Pressure coupling which is isotropic in the ``x`` and ``y``
1090 direction, but different in the ``z`` direction. This can be
1091 useful for membrane simulations. Two values each for
1092 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1093 ``x/y`` and ``z`` directions respectively.
1095 .. mdp-value:: anisotropic
1097 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1098 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1099 respectively. When the off-diagonal compressibilities are set to
1100 zero, a rectangular box will stay rectangular. Beware that
1101 anisotropic scaling can lead to extreme deformation of the
1104 .. mdp-value:: surface-tension
1106 Surface tension coupling for surfaces parallel to the
1107 xy-plane. Uses normal pressure coupling for the ``z``-direction,
1108 while the surface tension is coupled to the ``x/y`` dimensions of
1109 the box. The first :mdp:`ref-p` value is the reference surface
1110 tension times the number of surfaces ``bar nm``, the second
1111 value is the reference ``z``-pressure ``bar``. The two
1112 :mdp:`compressibility` values are the compressibility in the
1113 ``x/y`` and ``z`` direction respectively. The value for the
1114 ``z``-compressibility should be reasonably accurate since it
1115 influences the convergence of the surface-tension, it can also
1116 be set to zero to have a box with constant height.
1121 The frequency for coupling the pressure. The default value of -1
1122 sets :mdp:`nstpcouple` equal to 10, or fewer steps if required
1123 for accurate integration. Note that the default value is not 1
1124 because additional computation and communication is required for
1125 obtaining the virial. For velocity
1126 Verlet integrators :mdp:`nstpcouple` is set to 1.
1131 The time constant for pressure coupling (one value for all
1134 .. mdp:: compressibility
1137 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1138 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1139 required values is implied by :mdp:`pcoupltype`.
1144 The reference pressure for coupling. The number of required values
1145 is implied by :mdp:`pcoupltype`.
1147 .. mdp:: refcoord-scaling
1151 The reference coordinates for position restraints are not
1152 modified. Note that with this option the virial and pressure
1153 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1158 The reference coordinates are scaled with the scaling matrix of
1159 the pressure coupling.
1163 Scale the center of mass of the reference coordinates with the
1164 scaling matrix of the pressure coupling. The vectors of each
1165 reference coordinate to the center of mass are not scaled. Only
1166 one COM is used, even when there are multiple molecules with
1167 position restraints. For calculating the COM of the reference
1168 coordinates in the starting configuration, periodic boundary
1169 conditions are not taken into account. Note that with this option
1170 the virial and pressure might be ill defined, see
1171 :ref:`here <reference-manual-position-restraints>` for more details.
1177 Simulated annealing is controlled separately for each temperature
1178 group in |Gromacs|. The reference temperature is a piecewise linear
1179 function, but you can use an arbitrary number of points for each
1180 group, and choose either a single sequence or a periodic behaviour for
1181 each group. The actual annealing is performed by dynamically changing
1182 the reference temperature used in the thermostat algorithm selected,
1183 so remember that the system will usually not instantaneously reach the
1184 reference temperature!
1188 Type of annealing for each temperature group
1192 No simulated annealing - just couple to reference temperature value.
1194 .. mdp-value:: single
1196 A single sequence of annealing points. If your simulation is
1197 longer than the time of the last point, the temperature will be
1198 coupled to this constant value after the annealing sequence has
1199 reached the last time point.
1201 .. mdp-value:: periodic
1203 The annealing will start over at the first reference point once
1204 the last reference time is reached. This is repeated until the
1207 .. mdp:: annealing-npoints
1209 A list with the number of annealing reference/control points used
1210 for each temperature group. Use 0 for groups that are not
1211 annealed. The number of entries should equal the number of
1214 .. mdp:: annealing-time
1216 List of times at the annealing reference/control points for each
1217 group. If you are using periodic annealing, the times will be used
1218 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1219 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1220 etc. The number of entries should equal the sum of the numbers
1221 given in :mdp:`annealing-npoints`.
1223 .. mdp:: annealing-temp
1225 List of temperatures at the annealing reference/control points for
1226 each group. The number of entries should equal the sum of the
1227 numbers given in :mdp:`annealing-npoints`.
1229 Confused? OK, let's use an example. Assume you have two temperature
1230 groups, set the group selections to ``annealing = single periodic``,
1231 the number of points of each group to ``annealing-npoints = 3 4``, the
1232 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1233 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1234 will be coupled to 298K at 0ps, but the reference temperature will
1235 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1236 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1237 second group is coupled to 298K at 0ps, it increases linearly to 320K
1238 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1239 decreases to 298K, and then it starts over with the same pattern
1240 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1241 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1251 Do not generate velocities. The velocities are set to zero
1252 when there are no velocities in the input structure file.
1256 Generate velocities in :ref:`gmx grompp` according to a
1257 Maxwell distribution at temperature :mdp:`gen-temp`, with
1258 random seed :mdp:`gen-seed`. This is only meaningful with
1259 :mdp-value:`integrator=md`.
1264 temperature for Maxwell distribution
1269 used to initialize random generator for random velocities,
1270 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1277 .. mdp:: constraints
1279 Controls which bonds in the topology will be converted to rigid
1280 holonomic constraints. Note that typical rigid water models do not
1281 have bonds, but rather a specialized ``[settles]`` directive, so
1282 are not affected by this keyword.
1286 No bonds converted to constraints.
1288 .. mdp-value:: h-bonds
1290 Convert the bonds with H-atoms to constraints.
1292 .. mdp-value:: all-bonds
1294 Convert all bonds to constraints.
1296 .. mdp-value:: h-angles
1298 Convert all bonds to constraints and convert the angles that
1299 involve H-atoms to bond-constraints.
1301 .. mdp-value:: all-angles
1303 Convert all bonds to constraints and all angles to bond-constraints.
1305 .. mdp:: constraint-algorithm
1307 Chooses which solver satisfies any non-SETTLE holonomic
1310 .. mdp-value:: LINCS
1312 LINear Constraint Solver. With domain decomposition the parallel
1313 version P-LINCS is used. The accuracy in set with
1314 :mdp:`lincs-order`, which sets the number of matrices in the
1315 expansion for the matrix inversion. After the matrix inversion
1316 correction the algorithm does an iterative correction to
1317 compensate for lengthening due to rotation. The number of such
1318 iterations can be controlled with :mdp:`lincs-iter`. The root
1319 mean square relative constraint deviation is printed to the log
1320 file every :mdp:`nstlog` steps. If a bond rotates more than
1321 :mdp:`lincs-warnangle` in one step, a warning will be printed
1322 both to the log file and to ``stderr``. LINCS should not be used
1323 with coupled angle constraints.
1325 .. mdp-value:: SHAKE
1327 SHAKE is slightly slower and less stable than LINCS, but does
1328 work with angle constraints. The relative tolerance is set with
1329 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1330 does not support constraints between atoms on different
1331 decomposition domains, so it can only be used with domain
1332 decomposition when so-called update-groups are used, which is
1333 usally the case when only bonds involving hydrogens are
1334 constrained. SHAKE can not be used with energy minimization.
1336 .. mdp:: continuation
1338 This option was formerly known as ``unconstrained-start``.
1342 apply constraints to the start configuration and reset shells
1346 do not apply constraints to the start configuration and do not
1347 reset shells, useful for exact coninuation and reruns
1352 relative tolerance for SHAKE
1354 .. mdp:: lincs-order
1357 Highest order in the expansion of the constraint coupling
1358 matrix. When constraints form triangles, an additional expansion of
1359 the same order is applied on top of the normal expansion only for
1360 the couplings within such triangles. For "normal" MD simulations an
1361 order of 4 usually suffices, 6 is needed for large time-steps with
1362 virtual sites or BD. For accurate energy minimization an order of 8
1363 or more might be required. With domain decomposition, the cell size
1364 is limited by the distance spanned by :mdp:`lincs-order` +1
1365 constraints. When one wants to scale further than this limit, one
1366 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1367 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1368 )* :mdp:`lincs-order` remains constant.
1373 Number of iterations to correct for rotational lengthening in
1374 LINCS. For normal runs a single step is sufficient, but for NVE
1375 runs where you want to conserve energy accurately or for accurate
1376 energy minimization you might want to increase it to 2.
1378 .. mdp:: lincs-warnangle
1381 maximum angle that a bond can rotate before LINCS will complain
1387 bonds are represented by a harmonic potential
1391 bonds are represented by a Morse potential
1394 Energy group exclusions
1395 ^^^^^^^^^^^^^^^^^^^^^^^
1397 .. mdp:: energygrp-excl
1399 Pairs of energy groups for which all non-bonded interactions are
1400 excluded. An example: if you have two energy groups ``Protein`` and
1401 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1402 would give only the non-bonded interactions between the protein and
1403 the solvent. This is especially useful for speeding up energy
1404 calculations with ``mdrun -rerun`` and for excluding interactions
1405 within frozen groups.
1414 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1415 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1416 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1417 used (it is usually best to use semiisotropic pressure coupling
1418 with the ``x/y`` compressibility set to 0, as otherwise the surface
1419 area will change). Walls interact wit the rest of the system
1420 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1421 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1422 monitor the interaction of energy groups with each wall. The center
1423 of mass motion removal will be turned off in the ``z``-direction.
1425 .. mdp:: wall-atomtype
1427 the atom type name in the force field for each wall. By (for
1428 example) defining a special wall atom type in the topology with its
1429 own combination rules, this allows for independent tuning of the
1430 interaction of each atomtype with the walls.
1436 LJ integrated over the volume behind the wall: 9-3 potential
1440 LJ integrated over the wall surface: 10-4 potential
1444 direct LJ potential with the ``z`` distance from the wall
1448 user defined potentials indexed with the ``z`` distance from the
1449 wall, the tables are read analogously to the
1450 :mdp:`energygrp-table` option, where the first name is for a
1451 "normal" energy group and the second name is ``wall0`` or
1452 ``wall1``, only the dispersion and repulsion columns are used
1454 .. mdp:: wall-r-linpot
1457 Below this distance from the wall the potential is continued
1458 linearly and thus the force is constant. Setting this option to a
1459 postive value is especially useful for equilibration when some
1460 atoms are beyond a wall. When the value is <=0 (<0 for
1461 :mdp:`wall-type` =table), a fatal error is generated when atoms
1464 .. mdp:: wall-density
1466 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1467 the number density of the atoms for each wall for wall types 9-3
1470 .. mdp:: wall-ewald-zfac
1473 The scaling factor for the third box vector for Ewald summation
1474 only, the minimum is 2. Ewald summation can only be used with
1475 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1476 ``=3dc``. The empty layer in the box serves to decrease the
1477 unphysical Coulomb interaction between periodic images.
1483 Note that where pulling coordinates are applicable, there can be more
1484 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1485 variables will exist accordingly. Documentation references to things
1486 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1487 applicable pulling coordinate, eg. the second pull coordinate is described by
1488 pull-coord2-vec, pull-coord2-k, and so on.
1494 No center of mass pulling. All the following pull options will
1495 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1500 Center of mass pulling will be applied on 1 or more groups using
1501 1 or more pull coordinates.
1503 .. mdp:: pull-cylinder-r
1506 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1508 .. mdp:: pull-constr-tol
1511 the relative constraint tolerance for constraint pulling
1513 .. mdp:: pull-print-com
1517 do not print the COM for any group
1521 print the COM of all groups for all pull coordinates
1523 .. mdp:: pull-print-ref-value
1527 do not print the reference value for each pull coordinate
1531 print the reference value for each pull coordinate
1533 .. mdp:: pull-print-components
1537 only print the distance for each pull coordinate
1541 print the distance and Cartesian components selected in
1542 :mdp:`pull-coord1-dim`
1544 .. mdp:: pull-nstxout
1547 frequency for writing out the COMs of all the pull group (0 is
1550 .. mdp:: pull-nstfout
1553 frequency for writing out the force of all the pulled group
1556 .. mdp:: pull-pbc-ref-prev-step-com
1560 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1561 treatment of periodic boundary conditions.
1565 Use the COM of the previous step as reference for the treatment
1566 of periodic boundary conditions. The reference is initialized
1567 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1568 be located centrally in the group. Using the COM from the
1569 previous step can be useful if one or more pull groups are large.
1571 .. mdp:: pull-xout-average
1575 Write the instantaneous coordinates for all the pulled groups.
1579 Write the average coordinates (since last output) for all the
1580 pulled groups. N.b., some analysis tools might expect instantaneous
1583 .. mdp:: pull-fout-average
1587 Write the instantaneous force for all the pulled groups.
1591 Write the average force (since last output) for all the
1592 pulled groups. N.b., some analysis tools might expect instantaneous
1595 .. mdp:: pull-ngroups
1598 The number of pull groups, not including the absolute reference
1599 group, when used. Pull groups can be reused in multiple pull
1600 coordinates. Below only the pull options for group 1 are given,
1601 further groups simply increase the group index number.
1603 .. mdp:: pull-ncoords
1606 The number of pull coordinates. Below only the pull options for
1607 coordinate 1 are given, further coordinates simply increase the
1608 coordinate index number.
1610 .. mdp:: pull-group1-name
1612 The name of the pull group, is looked up in the index file or in
1613 the default groups to obtain the atoms involved.
1615 .. mdp:: pull-group1-weights
1617 Optional relative weights which are multiplied with the masses of
1618 the atoms to give the total weight for the COM. The number should
1619 be 0, meaning all 1, or the number of atoms in the pull group.
1621 .. mdp:: pull-group1-pbcatom
1624 The reference atom for the treatment of periodic boundary
1625 conditions inside the group (this has no effect on the treatment of
1626 the pbc between groups). This option is only important when the
1627 diameter of the pull group is larger than half the shortest box
1628 vector. For determining the COM, all atoms in the group are put at
1629 their periodic image which is closest to
1630 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1631 atom (number wise) is used, which is only safe for small groups.
1632 :ref:`gmx grompp` checks that the maximum distance from the reference
1633 atom (specifically chosen, or not) to the other atoms in the group
1634 is not too large. This parameter is not used with
1635 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1636 weighting, which is useful for a group of molecules in a periodic
1637 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1640 .. mdp:: pull-coord1-type
1642 .. mdp-value:: umbrella
1644 Center of mass pulling using an umbrella potential between the
1645 reference group and one or more groups.
1647 .. mdp-value:: constraint
1649 Center of mass pulling using a constraint between the reference
1650 group and one or more groups. The setup is identical to the
1651 option umbrella, except for the fact that a rigid constraint is
1652 applied instead of a harmonic potential.
1654 .. mdp-value:: constant-force
1656 Center of mass pulling using a linear potential and therefore a
1657 constant force. For this option there is no reference position
1658 and therefore the parameters :mdp:`pull-coord1-init` and
1659 :mdp:`pull-coord1-rate` are not used.
1661 .. mdp-value:: flat-bottom
1663 At distances above :mdp:`pull-coord1-init` a harmonic potential
1664 is applied, otherwise no potential is applied.
1666 .. mdp-value:: flat-bottom-high
1668 At distances below :mdp:`pull-coord1-init` a harmonic potential
1669 is applied, otherwise no potential is applied.
1671 .. mdp-value:: external-potential
1673 An external potential that needs to be provided by another
1676 .. mdp:: pull-coord1-potential-provider
1678 The name of the external module that provides the potential for
1679 the case where :mdp:`pull-coord1-type` is external-potential.
1681 .. mdp:: pull-coord1-geometry
1683 .. mdp-value:: distance
1685 Pull along the vector connecting the two groups. Components can
1686 be selected with :mdp:`pull-coord1-dim`.
1688 .. mdp-value:: direction
1690 Pull in the direction of :mdp:`pull-coord1-vec`.
1692 .. mdp-value:: direction-periodic
1694 As :mdp-value:`pull-coord1-geometry=direction`, but does not apply
1695 periodic box vector corrections to keep the distance within half
1696 the box length. This is (only) useful for pushing groups apart
1697 by more than half the box length by continuously changing the reference
1698 location using a pull rate. With this geometry the box should not be
1699 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1700 the pull force is not added to the virial.
1702 .. mdp-value:: direction-relative
1704 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1705 that points from the COM of a third to the COM of a fourth pull
1706 group. This means that 4 groups need to be supplied in
1707 :mdp:`pull-coord1-groups`. Note that the pull force will give
1708 rise to a torque on the pull vector, which is turn leads to
1709 forces perpendicular to the pull vector on the two groups
1710 defining the vector. If you want a pull group to move between
1711 the two groups defining the vector, simply use the union of
1712 these two groups as the reference group.
1714 .. mdp-value:: cylinder
1716 Designed for pulling with respect to a layer where the reference
1717 COM is given by a local cylindrical part of the reference group.
1718 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1719 the first of the two groups in :mdp:`pull-coord1-groups` a
1720 cylinder is selected around the axis going through the COM of
1721 the second group with direction :mdp:`pull-coord1-vec` with
1722 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1723 continously to zero as the radial distance goes from 0 to
1724 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1725 dependence gives rise to radial forces on both pull groups.
1726 Note that the radius should be smaller than half the box size.
1727 For tilted cylinders they should be even smaller than half the
1728 box size since the distance of an atom in the reference group
1729 from the COM of the pull group has both a radial and an axial
1730 component. This geometry is not supported with constraint
1733 .. mdp-value:: angle
1735 Pull along an angle defined by four groups. The angle is
1736 defined as the angle between two vectors: the vector connecting
1737 the COM of the first group to the COM of the second group and
1738 the vector connecting the COM of the third group to the COM of
1741 .. mdp-value:: angle-axis
1743 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1744 Thus, only the two groups that define the first vector need to be given.
1746 .. mdp-value:: dihedral
1748 Pull along a dihedral angle defined by six groups. These pairwise
1749 define three vectors: the vector connecting the COM of group 1
1750 to the COM of group 2, the COM of group 3 to the COM of group 4,
1751 and the COM of group 5 to the COM group 6. The dihedral angle is
1752 then defined as the angle between two planes: the plane spanned by the
1753 the two first vectors and the plane spanned the two last vectors.
1756 .. mdp:: pull-coord1-groups
1758 The group indices on which this pull coordinate will operate.
1759 The number of group indices required is geometry dependent.
1760 The first index can be 0, in which case an
1761 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1762 absolute reference the system is no longer translation invariant
1763 and one should think about what to do with the center of mass
1766 .. mdp:: pull-coord1-dim
1769 Selects the dimensions that this pull coordinate acts on and that
1770 are printed to the output files when
1771 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1772 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1773 components set to Y contribute to the distance. Thus setting this
1774 to Y Y N results in a distance in the x/y plane. With other
1775 geometries all dimensions with non-zero entries in
1776 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1777 dimensions only affect the output.
1779 .. mdp:: pull-coord1-origin
1782 The pull reference position for use with an absolute reference.
1784 .. mdp:: pull-coord1-vec
1787 The pull direction. :ref:`gmx grompp` normalizes the vector.
1789 .. mdp:: pull-coord1-start
1793 do not modify :mdp:`pull-coord1-init`
1797 add the COM distance of the starting conformation to
1798 :mdp:`pull-coord1-init`
1800 .. mdp:: pull-coord1-init
1803 The reference distance or reference angle at t=0.
1805 .. mdp:: pull-coord1-rate
1807 (0) [nm/ps] or [deg/ps]
1808 The rate of change of the reference position or reference angle.
1810 .. mdp:: pull-coord1-k
1812 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1813 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1814 The force constant. For umbrella pulling this is the harmonic force
1815 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1816 for angles). For constant force pulling this is the
1817 force constant of the linear potential, and thus the negative (!)
1818 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1819 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1820 Note that for angles the force constant is expressed in terms of radians
1821 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1823 .. mdp:: pull-coord1-kB
1825 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1826 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1827 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1828 :mdp:`free-energy` is turned on. The force constant is then (1 -
1829 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1831 AWH adaptive biasing
1832 ^^^^^^^^^^^^^^^^^^^^
1842 Adaptively bias a reaction coordinate using the AWH method and estimate
1843 the corresponding PMF. The PMF and other AWH data are written to energy
1844 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1845 the ``gmx awh`` tool. The AWH coordinate can be
1846 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1847 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1848 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1849 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1851 .. mdp:: awh-potential
1853 .. mdp-value:: convolved
1855 The applied biasing potential is the convolution of the bias function and a
1856 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1857 in a smooth potential function and force. The resolution of the potential is set
1858 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1860 .. mdp-value:: umbrella
1862 The potential bias is applied by controlling the position of an harmonic potential
1863 using Monte-Carlo sampling. The force constant is set with
1864 :mdp:`awh1-dim1-force-constant`. The umbrella location
1865 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1866 There are no advantages to using an umbrella.
1867 This option is mainly for comparison and testing purposes.
1869 .. mdp:: awh-share-multisim
1873 AWH will not share biases across simulations started with
1874 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1878 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1879 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1880 with the biases with the same :mdp:`awh1-share-group` value.
1881 The simulations should have the same AWH settings for sharing to make sense.
1882 :ref:`gmx mdrun` will check whether the simulations are technically
1883 compatible for sharing, but the user should check that bias sharing
1884 physically makes sense.
1888 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1889 where -1 indicates to generate a seed. Only used with
1890 :mdp-value:`awh-potential=umbrella`.
1895 Number of steps between printing AWH data to the energy file, should be
1896 a multiple of :mdp:`nstenergy`.
1898 .. mdp:: awh-nstsample
1901 Number of steps between sampling of the coordinate value. This sampling
1902 is the basis for updating the bias and estimating the PMF and other AWH observables.
1904 .. mdp:: awh-nsamples-update
1907 The number of coordinate samples used for each AWH update.
1908 The update interval in steps is :mdp:`awh-nstsample` times this value.
1913 The number of biases, each acting on its own coordinate.
1914 The following options should be specified
1915 for each bias although below only the options for bias number 1 is shown. Options for
1916 other bias indices are obtained by replacing '1' by the bias index.
1918 .. mdp:: awh1-error-init
1920 (10.0) [kJ mol\ :sup:`-1`]
1921 Estimated initial average error of the PMF for this bias. This value together with the
1922 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1923 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1925 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1926 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1927 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1928 then :mdp:`awh1-error-init` should reflect that knowledge.
1930 .. mdp:: awh1-growth
1932 .. mdp-value:: exp-linear
1934 Each bias keeps a reference weight histogram for the coordinate samples.
1935 Its size sets the magnitude of the bias function and free energy estimate updates
1936 (few samples corresponds to large updates and vice versa).
1937 Thus, its growth rate sets the maximum convergence rate.
1938 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1939 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1940 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1941 high free energy barriers have not yet been flattened by the bias.
1943 .. mdp-value:: linear
1945 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1946 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
1947 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
1949 .. mdp:: awh1-equilibrate-histogram
1953 Do not equilibrate histogram.
1957 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
1958 histogram of sampled weights is following the target distribution closely enough (specifically,
1959 at least 80% of the target region needs to have a local relative error of less than 20%). This
1960 option would typically only be used when :mdp:`awh1-share-group` > 0
1961 and the initial configurations poorly represent the target
1964 .. mdp:: awh1-target
1966 .. mdp-value:: constant
1968 The bias is tuned towards a constant (uniform) coordinate distribution
1969 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
1971 .. mdp-value:: cutoff
1973 Similar to :mdp-value:`awh1-target=constant`, but the target
1974 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
1975 where F is the free energy relative to the estimated global minimum.
1976 This provides a smooth switch of a flat target distribution in
1977 regions with free energy lower than the cut-off to a Boltzmann
1978 distribution in regions with free energy higher than the cut-off.
1980 .. mdp-value:: boltzmann
1982 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
1983 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
1984 would give the same coordinate distribution as sampling with a simulation temperature
1987 .. mdp-value:: local-boltzmann
1989 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
1990 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
1991 change of the bias only depends on the local sampling. This local convergence property is
1992 only compatible with :mdp-value:`awh1-growth=linear`, since for
1993 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
1995 .. mdp:: awh1-target-beta-scaling
1998 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
1999 it is the unitless beta scaling factor taking values in (0,1).
2001 .. mdp:: awh1-target-cutoff
2003 (0) [kJ mol\ :sup:`-1`]
2004 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2006 .. mdp:: awh1-user-data
2010 Initialize the PMF and target distribution with default values.
2014 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2015 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2016 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2017 The file name can be changed with the ``-awh`` option.
2018 The first :mdp:`awh1-ndim` columns of
2019 each input file should contain the coordinate values, such that each row defines a point in
2020 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value (in kT) for each point.
2021 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2022 be in the same column as written by :ref:`gmx awh`.
2024 .. mdp:: awh1-share-group
2028 Do not share the bias.
2030 .. mdp-value:: positive
2032 Share the bias and PMF estimates within and/or between simulations.
2033 Within a simulation, the bias will be shared between biases that have the
2034 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2035 With :mdp-value:`awh-share-multisim=yes` and
2036 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2037 Sharing may increase convergence initially, although the starting configurations
2038 can be critical, especially when sharing between many biases.
2039 Currently, positive group values should start at 1 and increase
2040 by 1 for each subsequent bias that is shared.
2045 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2046 The following options should be specified for each such dimension. Below only
2047 the options for dimension number 1 is shown. Options for other dimension indices are
2048 obtained by replacing '1' by the dimension index.
2050 .. mdp:: awh1-dim1-coord-provider
2054 The pull module is providing the reaction coordinate for this dimension.
2056 .. mdp-value:: fep-lambda
2058 The free energy lambda state is the reaction coordinate for this dimension.
2059 The lambda states to use are specified by :mdp:`fep-lambdas`, :mdp:`vdw-lambdas`,
2060 :mdp:`coul-lambdas` etc. This is not compatible with delta-lambda. It also requires
2061 calc-lambda-neighbors to be -1.
2063 .. mdp:: awh1-dim1-coord-index
2066 Index of the pull coordinate defining this coordinate dimension.
2068 .. mdp:: awh1-dim1-force-constant
2070 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2071 Force constant for the (convolved) umbrella potential(s) along this
2072 coordinate dimension.
2074 .. mdp:: awh1-dim1-start
2077 Start value of the sampling interval along this dimension. The range of allowed
2078 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2079 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2080 is allowed. The interval will then wrap around from +period/2 to -period/2.
2081 For the direction geometry, the dimension is made periodic when
2082 the direction is along a box vector and covers more than 95%
2083 of the box length. Note that one should not apply pressure coupling
2084 along a periodic dimension.
2086 .. mdp:: awh1-dim1-end
2089 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2091 .. mdp:: awh1-dim1-diffusion
2093 (10\ :sup:`-5`) [nm\ :sup:`2`/ps], [rad\ :sup:`2`/ps] or [ps\ :sup:`-1`]
2094 Estimated diffusion constant for this coordinate dimension determining the initial
2095 biasing rate. This needs only be a rough estimate and should not critically
2096 affect the results unless it is set to something very low, leading to slow convergence,
2097 or very high, forcing the system far from equilibrium. Not setting this value
2098 explicitly generates a warning.
2100 .. mdp:: awh1-dim1-cover-diameter
2103 Diameter that needs to be sampled by a single simulation around a coordinate value
2104 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2105 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2106 across each coordinate value.
2107 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2108 (:mdp:`awh1-share-group`>0).
2109 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2110 for many sharing simulations does not guarantee transitions across free energy barriers.
2111 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2112 has independently sampled the whole interval.
2117 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2118 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2119 that can be used to achieve such a rotation.
2125 No enforced rotation will be applied. All enforced rotation options will
2126 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2131 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2132 under the :mdp:`rot-group0` option.
2134 .. mdp:: rot-ngroups
2137 Number of rotation groups.
2141 Name of rotation group 0 in the index file.
2146 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2147 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2148 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2153 Use mass weighted rotation group positions.
2158 Rotation vector, will get normalized.
2163 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2167 (0) [degree ps\ :sup:`-1`]
2168 Reference rotation rate of group 0.
2172 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2173 Force constant for group 0.
2175 .. mdp:: rot-slab-dist0
2178 Slab distance, if a flexible axis rotation type was chosen.
2180 .. mdp:: rot-min-gauss0
2183 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2184 (for the flexible axis potentials).
2188 (0.0001) [nm\ :sup:`2`]
2189 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2191 .. mdp:: rot-fit-method0
2194 Fitting method when determining the actual angle of a rotation group
2195 (can be one of ``rmsd``, ``norm``, or ``potential``).
2197 .. mdp:: rot-potfit-nsteps0
2200 For fit type ``potential``, the number of angular positions around the reference angle for which the
2201 rotation potential is evaluated.
2203 .. mdp:: rot-potfit-step0
2206 For fit type ``potential``, the distance in degrees between two angular positions.
2208 .. mdp:: rot-nstrout
2211 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2212 and the rotation potential energy.
2214 .. mdp:: rot-nstsout
2217 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2227 ignore distance restraint information in topology file
2229 .. mdp-value:: simple
2231 simple (per-molecule) distance restraints.
2233 .. mdp-value:: ensemble
2235 distance restraints over an ensemble of molecules in one
2236 simulation box. Normally, one would perform ensemble averaging
2237 over multiple simulations, using ``mdrun
2238 -multidir``. The environment
2239 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2240 within each ensemble (usually equal to the number of directories
2241 supplied to ``mdrun -multidir``).
2243 .. mdp:: disre-weighting
2245 .. mdp-value:: equal
2247 divide the restraint force equally over all atom pairs in the
2250 .. mdp-value:: conservative
2252 the forces are the derivative of the restraint potential, this
2253 results in an weighting of the atom pairs to the reciprocal
2254 seventh power of the displacement. The forces are conservative
2255 when :mdp:`disre-tau` is zero.
2257 .. mdp:: disre-mixed
2261 the violation used in the calculation of the restraint force is
2262 the time-averaged violation
2266 the violation used in the calculation of the restraint force is
2267 the square root of the product of the time-averaged violation
2268 and the instantaneous violation
2272 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2273 force constant for distance restraints, which is multiplied by a
2274 (possibly) different factor for each restraint given in the ``fac``
2275 column of the interaction in the topology file.
2280 time constant for distance restraints running average. A value of
2281 zero turns off time averaging.
2283 .. mdp:: nstdisreout
2286 period between steps when the running time-averaged and
2287 instantaneous distances of all atom pairs involved in restraints
2288 are written to the energy file (can make the energy file very
2295 ignore orientation restraint information in topology file
2299 use orientation restraints, ensemble averaging can be performed
2300 with ``mdrun -multidir``
2304 (0) [kJ mol\ :sup:`-1`]
2305 force constant for orientation restraints, which is multiplied by a
2306 (possibly) different weight factor for each restraint, can be set
2307 to zero to obtain the orientations from a free simulation
2312 time constant for orientation restraints running average. A value
2313 of zero turns off time averaging.
2315 .. mdp:: orire-fitgrp
2317 fit group for orientation restraining. This group of atoms is used
2318 to determine the rotation **R** of the system with respect to the
2319 reference orientation. The reference orientation is the starting
2320 conformation of the first subsystem. For a protein, backbone is a
2323 .. mdp:: nstorireout
2326 period between steps when the running time-averaged and
2327 instantaneous orientations for all restraints, and the molecular
2328 order tensor are written to the energy file (can make the energy
2332 Free energy calculations
2333 ^^^^^^^^^^^^^^^^^^^^^^^^
2335 .. mdp:: free-energy
2339 Only use topology A.
2343 Interpolate between topology A (lambda=0) to topology B
2344 (lambda=1) and write the derivative of the Hamiltonian with
2345 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2346 or the Hamiltonian differences with respect to other lambda
2347 values (as specified with foreign lambda) to the energy file
2348 and/or to ``dhdl.xvg``, where they can be processed by, for
2349 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2350 are interpolated linearly as described in the manual. When
2351 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2352 used for the LJ and Coulomb interactions.
2356 Turns on expanded ensemble simulation, where the alchemical state
2357 becomes a dynamic variable, allowing jumping between different
2358 Hamiltonians. See the expanded ensemble options for controlling how
2359 expanded ensemble simulations are performed. The different
2360 Hamiltonians used in expanded ensemble simulations are defined by
2361 the other free energy options.
2363 .. mdp:: init-lambda
2366 starting value for lambda (float). Generally, this should only be
2367 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2368 other cases, :mdp:`init-lambda-state` should be specified
2369 instead. Must be greater than or equal to 0.
2371 .. mdp:: delta-lambda
2374 increment per time step for lambda
2376 .. mdp:: init-lambda-state
2379 starting value for the lambda state (integer). Specifies which
2380 columm of the lambda vector (:mdp:`coul-lambdas`,
2381 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2382 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2383 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2384 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2385 the first column, and so on.
2387 .. mdp:: fep-lambdas
2390 Zero, one or more lambda values for which Delta H values will be
2391 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2392 steps. Values must be between 0 and 1. Free energy differences
2393 between different lambda values can then be determined with
2394 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2395 other -lambdas keywords because all components of the lambda vector
2396 that are not specified will use :mdp:`fep-lambdas` (including
2397 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2399 .. mdp:: coul-lambdas
2402 Zero, one or more lambda values for which Delta H values will be
2403 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2404 steps. Values must be between 0 and 1. Only the electrostatic
2405 interactions are controlled with this component of the lambda
2406 vector (and only if the lambda=0 and lambda=1 states have differing
2407 electrostatic interactions).
2409 .. mdp:: vdw-lambdas
2412 Zero, one or more lambda values for which Delta H values will be
2413 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2414 steps. Values must be between 0 and 1. Only the van der Waals
2415 interactions are controlled with this component of the lambda
2418 .. mdp:: bonded-lambdas
2421 Zero, one or more lambda values for which Delta H values will be
2422 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2423 steps. Values must be between 0 and 1. Only the bonded interactions
2424 are controlled with this component of the lambda vector.
2426 .. mdp:: restraint-lambdas
2429 Zero, one or more lambda values for which Delta H values will be
2430 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2431 steps. Values must be between 0 and 1. Only the restraint
2432 interactions: dihedral restraints, and the pull code restraints are
2433 controlled with this component of the lambda vector.
2435 .. mdp:: mass-lambdas
2438 Zero, one or more lambda values for which Delta H values will be
2439 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2440 steps. Values must be between 0 and 1. Only the particle masses are
2441 controlled with this component of the lambda vector.
2443 .. mdp:: temperature-lambdas
2446 Zero, one or more lambda values for which Delta H values will be
2447 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2448 steps. Values must be between 0 and 1. Only the temperatures
2449 controlled with this component of the lambda vector. Note that
2450 these lambdas should not be used for replica exchange, only for
2451 simulated tempering.
2453 .. mdp:: calc-lambda-neighbors
2456 Controls the number of lambda values for which Delta H values will
2457 be calculated and written out, if :mdp:`init-lambda-state` has
2458 been set. A positive value will limit the number of lambda points
2459 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2460 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2461 has a value of 2, energies for lambda points 3-7 will be calculated
2462 and writen out. A value of -1 means all lambda points will be
2463 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2464 1 is sufficient, while for MBAR -1 should be used.
2469 the soft-core alpha parameter, a value of 0 results in linear
2470 interpolation of the LJ and Coulomb interactions
2475 power 6 for the radial term in the soft-core equation.
2480 Whether to apply the soft-core free energy interaction
2481 transformation to the Columbic interaction of a molecule. Default
2482 is no, as it is generally more efficient to turn off the Coulomic
2483 interactions linearly before turning off the van der Waals
2484 interactions. Note that it is only taken into account when lambda
2485 states are used, not with :mdp:`couple-lambda0` /
2486 :mdp:`couple-lambda1`, and you can still turn off soft-core
2487 interactions by setting :mdp:`sc-alpha` to 0.
2492 the power for lambda in the soft-core function, only the values 1
2498 the soft-core sigma for particles which have a C6 or C12 parameter
2499 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2501 .. mdp:: couple-moltype
2503 Here one can supply a molecule type (as defined in the topology)
2504 for calculating solvation or coupling free energies. There is a
2505 special option ``system`` that couples all molecule types in the
2506 system. This can be useful for equilibrating a system starting from
2507 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2508 on. The Van der Waals interactions and/or charges in this molecule
2509 type can be turned on or off between lambda=0 and lambda=1,
2510 depending on the settings of :mdp:`couple-lambda0` and
2511 :mdp:`couple-lambda1`. If you want to decouple one of several
2512 copies of a molecule, you need to copy and rename the molecule
2513 definition in the topology.
2515 .. mdp:: couple-lambda0
2517 .. mdp-value:: vdw-q
2519 all interactions are on at lambda=0
2523 the charges are zero (no Coulomb interactions) at lambda=0
2527 the Van der Waals interactions are turned at lambda=0; soft-core
2528 interactions will be required to avoid singularities
2532 the Van der Waals interactions are turned off and the charges
2533 are zero at lambda=0; soft-core interactions will be required to
2534 avoid singularities.
2536 .. mdp:: couple-lambda1
2538 analogous to :mdp:`couple-lambda1`, but for lambda=1
2540 .. mdp:: couple-intramol
2544 All intra-molecular non-bonded interactions for moleculetype
2545 :mdp:`couple-moltype` are replaced by exclusions and explicit
2546 pair interactions. In this manner the decoupled state of the
2547 molecule corresponds to the proper vacuum state without
2548 periodicity effects.
2552 The intra-molecular Van der Waals and Coulomb interactions are
2553 also turned on/off. This can be useful for partitioning
2554 free-energies of relatively large molecules, where the
2555 intra-molecular non-bonded interactions might lead to
2556 kinetically trapped vacuum conformations. The 1-4 pair
2557 interactions are not turned off.
2562 the frequency for writing dH/dlambda and possibly Delta H to
2563 dhdl.xvg, 0 means no ouput, should be a multiple of
2564 :mdp:`nstcalcenergy`.
2566 .. mdp:: dhdl-derivatives
2570 If yes (the default), the derivatives of the Hamiltonian with
2571 respect to lambda at each :mdp:`nstdhdl` step are written
2572 out. These values are needed for interpolation of linear energy
2573 differences with :ref:`gmx bar` (although the same can also be
2574 achieved with the right foreign lambda setting, that may not be as
2575 flexible), or with thermodynamic integration
2577 .. mdp:: dhdl-print-energy
2581 Include either the total or the potential energy in the dhdl
2582 file. Options are 'no', 'potential', or 'total'. This information
2583 is needed for later free energy analysis if the states of interest
2584 are at different temperatures. If all states are at the same
2585 temperature, this information is not needed. 'potential' is useful
2586 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2587 file. When rerunning from an existing trajectory, the kinetic
2588 energy will often not be correct, and thus one must compute the
2589 residual free energy from the potential alone, with the kinetic
2590 energy component computed analytically.
2592 .. mdp:: separate-dhdl-file
2596 The free energy values that are calculated (as specified with
2597 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2598 written out to a separate file, with the default name
2599 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2604 The free energy values are written out to the energy output file
2605 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2606 steps), where they can be extracted with :ref:`gmx energy` or
2607 used directly with :ref:`gmx bar`.
2609 .. mdp:: dh-hist-size
2612 If nonzero, specifies the size of the histogram into which the
2613 Delta H values (specified with foreign lambda) and the derivative
2614 dH/dl values are binned, and written to ener.edr. This can be used
2615 to save disk space while calculating free energy differences. One
2616 histogram gets written for each foreign lambda and two for the
2617 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2618 histogram settings (too small size or too wide bins) can introduce
2619 errors. Do not use histograms unless you're certain you need it.
2621 .. mdp:: dh-hist-spacing
2624 Specifies the bin width of the histograms, in energy units. Used in
2625 conjunction with :mdp:`dh-hist-size`. This size limits the
2626 accuracy with which free energies can be calculated. Do not use
2627 histograms unless you're certain you need it.
2630 Expanded Ensemble calculations
2631 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2633 .. mdp:: nstexpanded
2635 The number of integration steps beween attempted moves changing the
2636 system Hamiltonian in expanded ensemble simulations. Must be a
2637 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2644 No Monte Carlo in state space is performed.
2646 .. mdp-value:: metropolis-transition
2648 Uses the Metropolis weights to update the expanded ensemble
2649 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2652 .. mdp-value:: barker-transition
2654 Uses the Barker transition critera to update the expanded
2655 ensemble weight of each state i, defined by exp(-beta_new
2656 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2658 .. mdp-value:: wang-landau
2660 Uses the Wang-Landau algorithm (in state space, not energy
2661 space) to update the expanded ensemble weights.
2663 .. mdp-value:: min-variance
2665 Uses the minimum variance updating method of Escobedo et al. to
2666 update the expanded ensemble weights. Weights will not be the
2667 free energies, but will rather emphasize states that need more
2668 sampling to give even uncertainty.
2670 .. mdp:: lmc-mc-move
2674 No Monte Carlo in state space is performed.
2676 .. mdp-value:: metropolis-transition
2678 Randomly chooses a new state up or down, then uses the
2679 Metropolis critera to decide whether to accept or reject:
2680 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2682 .. mdp-value:: barker-transition
2684 Randomly chooses a new state up or down, then uses the Barker
2685 transition critera to decide whether to accept or reject:
2686 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2688 .. mdp-value:: gibbs
2690 Uses the conditional weights of the state given the coordinate
2691 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2694 .. mdp-value:: metropolized-gibbs
2696 Uses the conditional weights of the state given the coordinate
2697 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2698 to move to, EXCLUDING the current state, then uses a rejection
2699 step to ensure detailed balance. Always more efficient that
2700 Gibbs, though only marginally so in many situations, such as
2701 when only the nearest neighbors have decent phase space
2707 random seed to use for Monte Carlo moves in state space. When
2708 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2710 .. mdp:: mc-temperature
2712 Temperature used for acceptance/rejection for Monte Carlo moves. If
2713 not specified, the temperature of the simulation specified in the
2714 first group of :mdp:`ref-t` is used.
2719 The cutoff for the histogram of state occupancies to be reset, and
2720 the free energy incrementor to be changed from delta to delta *
2721 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2722 each histogram) / (average number of samples at each
2723 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2724 histogram is only considered flat if all Nratio > 0.8 AND
2725 simultaneously all 1/Nratio > 0.8.
2730 Each time the histogram is considered flat, then the current value
2731 of the Wang-Landau incrementor for the free energies is multiplied
2732 by :mdp:`wl-scale`. Value must be between 0 and 1.
2734 .. mdp:: init-wl-delta
2737 The initial value of the Wang-Landau incrementor in kT. Some value
2738 near 1 kT is usually most efficient, though sometimes a value of
2739 2-3 in units of kT works better if the free energy differences are
2742 .. mdp:: wl-oneovert
2745 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2746 the large sample limit. There is significant evidence that the
2747 standard Wang-Landau algorithms in state space presented here
2748 result in free energies getting 'burned in' to incorrect values
2749 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2750 then when the incrementor becomes less than 1/N, where N is the
2751 mumber of samples collected (and thus proportional to the data
2752 collection time, hence '1 over t'), then the Wang-Lambda
2753 incrementor is set to 1/N, decreasing every step. Once this occurs,
2754 :mdp:`wl-ratio` is ignored, but the weights will still stop
2755 updating when the equilibration criteria set in
2756 :mdp:`lmc-weights-equil` is achieved.
2758 .. mdp:: lmc-repeats
2761 Controls the number of times that each Monte Carlo swap type is
2762 performed each iteration. In the limit of large numbers of Monte
2763 Carlo repeats, then all methods converge to Gibbs sampling. The
2764 value will generally not need to be different from 1.
2766 .. mdp:: lmc-gibbsdelta
2769 Limit Gibbs sampling to selected numbers of neighboring states. For
2770 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2771 sampling over all of the states that are defined. A positive value
2772 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2773 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2774 value of -1 means that all states are considered. For less than 100
2775 states, it is probably not that expensive to include all states.
2777 .. mdp:: lmc-forced-nstart
2780 Force initial state space sampling to generate weights. In order to
2781 come up with reasonable initial weights, this setting allows the
2782 simulation to drive from the initial to the final lambda state,
2783 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2784 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2785 sufficiently long (thousands of steps, perhaps), then the weights
2786 will be close to correct. However, in most cases, it is probably
2787 better to simply run the standard weight equilibration algorithms.
2789 .. mdp:: nst-transition-matrix
2792 Frequency of outputting the expanded ensemble transition matrix. A
2793 negative number means it will only be printed at the end of the
2796 .. mdp:: symmetrized-transition-matrix
2799 Whether to symmetrize the empirical transition matrix. In the
2800 infinite limit the matrix will be symmetric, but will diverge with
2801 statistical noise for short timescales. Forced symmetrization, by
2802 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2803 like the existence of (small magnitude) negative eigenvalues.
2805 .. mdp:: mininum-var-min
2808 The min-variance strategy (option of :mdp:`lmc-stats` is only
2809 valid for larger number of samples, and can get stuck if too few
2810 samples are used at each state. :mdp:`mininum-var-min` is the
2811 minimum number of samples that each state that are allowed before
2812 the min-variance strategy is activated if selected.
2814 .. mdp:: init-lambda-weights
2816 The initial weights (free energies) used for the expanded ensemble
2817 states. Default is a vector of zero weights. format is similar to
2818 the lambda vector settings in :mdp:`fep-lambdas`, except the
2819 weights can be any floating point number. Units are kT. Its length
2820 must match the lambda vector lengths.
2822 .. mdp:: lmc-weights-equil
2826 Expanded ensemble weights continue to be updated throughout the
2831 The input expanded ensemble weights are treated as equilibrated,
2832 and are not updated throughout the simulation.
2834 .. mdp-value:: wl-delta
2836 Expanded ensemble weight updating is stopped when the
2837 Wang-Landau incrementor falls below this value.
2839 .. mdp-value:: number-all-lambda
2841 Expanded ensemble weight updating is stopped when the number of
2842 samples at all of the lambda states is greater than this value.
2844 .. mdp-value:: number-steps
2846 Expanded ensemble weight updating is stopped when the number of
2847 steps is greater than the level specified by this value.
2849 .. mdp-value:: number-samples
2851 Expanded ensemble weight updating is stopped when the number of
2852 total samples across all lambda states is greater than the level
2853 specified by this value.
2855 .. mdp-value:: count-ratio
2857 Expanded ensemble weight updating is stopped when the ratio of
2858 samples at the least sampled lambda state and most sampled
2859 lambda state greater than this value.
2861 .. mdp:: simulated-tempering
2864 Turn simulated tempering on or off. Simulated tempering is
2865 implemented as expanded ensemble sampling with different
2866 temperatures instead of different Hamiltonians.
2868 .. mdp:: sim-temp-low
2871 Low temperature for simulated tempering.
2873 .. mdp:: sim-temp-high
2876 High temperature for simulated tempering.
2878 .. mdp:: simulated-tempering-scaling
2880 Controls the way that the temperatures at intermediate lambdas are
2881 calculated from the :mdp:`temperature-lambdas` part of the lambda
2884 .. mdp-value:: linear
2886 Linearly interpolates the temperatures using the values of
2887 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2888 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2889 a temperature of 350. A nonlinear set of temperatures can always
2890 be implemented with uneven spacing in lambda.
2892 .. mdp-value:: geometric
2894 Interpolates temperatures geometrically between
2895 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2896 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2897 :mdp:`sim-temp-low`) raised to the power of
2898 (i/(ntemps-1)). This should give roughly equal exchange for
2899 constant heat capacity, though of course things simulations that
2900 involve protein folding have very high heat capacity peaks.
2902 .. mdp-value:: exponential
2904 Interpolates temperatures exponentially between
2905 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2906 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2907 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2908 (i))-1)/(exp(1.0)-i)).
2916 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2917 in groups Protein and Sol will experience constant acceleration as
2918 specified in the :mdp:`accelerate` line
2922 (0) [nm ps\ :sup:`-2`]
2923 acceleration for :mdp:`acc-grps`; x, y and z for each group
2924 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2925 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
2930 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2931 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2932 specifies for which dimension(s) the freezing applies. To avoid
2933 spurious contributions to the virial and pressure due to large
2934 forces between completely frozen atoms you need to use energy group
2935 exclusions, this also saves computing time. Note that coordinates
2936 of frozen atoms are not scaled by pressure-coupling algorithms.
2940 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2941 specify ``Y`` or ``N`` for X, Y and Z and for each group (*e.g.*
2942 ``Y Y N N N N`` means that particles in the first group can move only in
2943 Z direction. The particles in the second group can move in any
2946 .. mdp:: cos-acceleration
2948 (0) [nm ps\ :sup:`-2`]
2949 the amplitude of the acceleration profile for calculating the
2950 viscosity. The acceleration is in the X-direction and the magnitude
2951 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2952 added to the energy file: the amplitude of the velocity profile and
2957 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
2958 The velocities of deformation for the box elements: a(x) b(y) c(z)
2959 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2960 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2961 elements are corrected for periodicity. The coordinates are
2962 transformed accordingly. Frozen degrees of freedom are (purposely)
2963 also transformed. The time ts is set to t at the first step and at
2964 steps at which x and v are written to trajectory to ensure exact
2965 restarts. Deformation can be used together with semiisotropic or
2966 anisotropic pressure coupling when the appropriate
2967 compressibilities are set to zero. The diagonal elements can be
2968 used to strain a solid. The off-diagonal elements can be used to
2969 shear a solid or a liquid.
2975 .. mdp:: electric-field-x
2976 .. mdp:: electric-field-y
2977 .. mdp:: electric-field-z
2979 Here you can specify an electric field that optionally can be
2980 alternating and pulsed. The general expression for the field
2981 has the form of a gaussian laser pulse:
2983 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
2985 For example, the four parameters for direction x are set in the
2986 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
2987 and ``electric-field-z``) like
2989 ``electric-field-x = E0 omega t0 sigma``
2991 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
2993 In the special case that ``sigma = 0``, the exponential term is omitted
2994 and only the cosine term is used. If also ``omega = 0`` a static
2995 electric field is applied.
2997 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
3000 Mixed quantum/classical molecular dynamics
3001 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3005 groups to be descibed at the QM level for MiMiC QM/MM
3011 QM/MM is no longer supported via these .mdp options. For MiMic, use no here.
3013 Computational Electrophysiology
3014 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3015 Use these options to switch on and control ion/water position exchanges in "Computational
3016 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3022 Do not enable ion/water position exchanges.
3024 .. mdp-value:: X ; Y ; Z
3026 Allow for ion/water position exchanges along the chosen direction.
3027 In a typical setup with the membranes parallel to the x-y plane,
3028 ion/water pairs need to be exchanged in Z direction to sustain the
3029 requested ion concentrations in the compartments.
3031 .. mdp:: swap-frequency
3033 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3034 per compartment are determined and exchanges made if necessary.
3035 Normally it is not necessary to check at every time step.
3036 For typical Computational Electrophysiology setups, a value of about 100 is
3037 sufficient and yields a negligible performance impact.
3039 .. mdp:: split-group0
3041 Name of the index group of the membrane-embedded part of channel #0.
3042 The center of mass of these atoms defines one of the compartment boundaries
3043 and should be chosen such that it is near the center of the membrane.
3045 .. mdp:: split-group1
3047 Channel #1 defines the position of the other compartment boundary.
3049 .. mdp:: massw-split0
3051 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3055 Use the geometrical center.
3059 Use the center of mass.
3061 .. mdp:: massw-split1
3063 (no) As above, but for split-group #1.
3065 .. mdp:: solvent-group
3067 Name of the index group of solvent molecules.
3069 .. mdp:: coupl-steps
3071 (10) Average the number of ions per compartment over these many swap attempt steps.
3072 This can be used to prevent that ions near a compartment boundary
3073 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3077 (1) The number of different ion types to be controlled. These are during the
3078 simulation exchanged with solvent molecules to reach the desired reference numbers.
3080 .. mdp:: iontype0-name
3082 Name of the first ion type.
3084 .. mdp:: iontype0-in-A
3086 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3087 The default value of -1 means: use the number of ions as found in time step 0
3090 .. mdp:: iontype0-in-B
3092 (-1) Reference number of ions of type 0 for compartment B.
3094 .. mdp:: bulk-offsetA
3096 (0.0) Offset of the first swap layer from the compartment A midplane.
3097 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3098 at maximum distance (= bulk concentration) to the split group layers. However,
3099 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3100 towards one of the compartment-partitioning layers (at +/- 1.0).
3102 .. mdp:: bulk-offsetB
3104 (0.0) Offset of the other swap layer from the compartment B midplane.
3109 (\1) Only swap ions if threshold difference to requested count is reached.
3113 (2.0) [nm] Radius of the split cylinder #0.
3114 Two split cylinders (mimicking the channel pores) can optionally be defined
3115 relative to the center of the split group. With the help of these cylinders
3116 it can be counted which ions have passed which channel. The split cylinder
3117 definition has no impact on whether or not ion/water swaps are done.
3121 (1.0) [nm] Upper extension of the split cylinder #0.
3125 (1.0) [nm] Lower extension of the split cylinder #0.
3129 (2.0) [nm] Radius of the split cylinder #1.
3133 (1.0) [nm] Upper extension of the split cylinder #1.
3137 (1.0) [nm] Lower extension of the split cylinder #1.
3139 Density-guided simulations
3140 ^^^^^^^^^^^^^^^^^^^^^^^^^^
3142 These options enable and control the calculation and application of additional
3143 forces that are derived from three-dimensional densities, e.g., from cryo
3144 electron-microscopy experiments. (See the `reference manual`_ for details)
3146 .. mdp:: density-guided-simulation-active
3148 (no) Activate density-guided simulations.
3150 .. mdp:: density-guided-simulation-group
3152 (protein) The atoms that are subject to the forces from the density-guided
3153 simulation and contribute to the simulated density.
3155 .. mdp:: density-guided-simulation-similarity-measure
3157 (inner-product) Similarity measure between the density that is calculated
3158 from the atom positions and the reference density.
3160 .. mdp-value:: inner-product
3162 Takes the sum of the product of reference density and simulated density
3165 .. mdp-value:: relative-entropy
3167 Uses the negative relative entropy (or Kullback-Leibler divergence)
3168 between reference density and simulated density as similarity measure.
3169 Negative density values are ignored.
3171 .. mdp-value:: cross-correlation
3173 Uses the Pearson correlation coefficient between reference density and
3174 simulated density as similarity measure.
3176 .. mdp:: density-guided-simulation-atom-spreading-weight
3178 (unity) Determines the multiplication factor for the Gaussian kernel when
3179 spreading atoms on the grid.
3181 .. mdp-value:: unity
3183 Every atom in the density fitting group is assigned the same unit factor.
3187 Atoms contribute to the simulated density proportional to their mass.
3189 .. mdp-value:: charge
3191 Atoms contribute to the simulated density proportional to their charge.
3193 .. mdp:: density-guided-simulation-force-constant
3195 (1e+09) [kJ mol\ :sup:`-1`] The scaling factor for density-guided simulation
3196 forces. May also be negative.
3198 .. mdp:: density-guided-simulation-gaussian-transform-spreading-width
3200 (0.2) [nm] The Gaussian RMS width for the spread kernel for the simulated
3203 .. mdp:: density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width
3205 (4) The range after which the gaussian is cut off in multiples of the Gaussian
3206 RMS width described above.
3208 .. mdp:: density-guided-simulation-reference-density-filename
3210 (reference.mrc) Reference density file name using an absolute path or a path
3211 relative to the to the folder from which :ref:`gmx mdrun` is called.
3213 .. mdp:: density-guided-simulation-nst
3215 (1) Interval in steps at which the density fitting forces are evaluated
3216 and applied. The forces are scaled by this number when applied (See the
3217 `reference manual`_ for details).
3219 .. mdp:: density-guided-simulation-normalize-densities
3221 (true) Normalize the sum of density voxel values to one for the reference
3222 density as well as the simulated density.
3224 .. mdp:: density-guided-simulation-adaptive-force-scaling
3226 (false) Adapt the force constant to ensure a steady increase in similarity
3227 between simulated and reference density.
3231 Do not use adaptive force scaling.
3235 Use adaptive force scaling.
3237 .. mdp:: density-guided-simulation-adaptive-force-scaling-time-constant
3239 (4) [ps] Couple force constant to increase in similarity with reference density
3240 with this time constant. Larger times result in looser coupling.
3242 .. mdp:: density-guided-simulation-shift-vector
3244 (0,0,0) [nm] Add this vector to all atoms in the
3245 density-guided-simulation-group before calculating forces and energies for
3246 density-guided-simulations. Affects only the density-guided-simulation forces
3247 and energies. Corresponds to a shift of the input density in the opposite
3248 direction by (-1) * density-guided-simulation-shift-vector.
3250 .. mdp:: density-guided-simulation-transformation-matrix
3252 (1,0,0,0,1,0,0,0,1) Multiply all atoms with this matrix in the
3253 density-guided-simulation-group before calculating forces and energies for
3254 density-guided-simulations. Affects only the density-guided-simulation forces
3255 and energies. Corresponds to a transformation of the input density by the
3256 inverse of this matrix. The matrix is given in row-major order.
3257 This option allows, e.g., rotation of the density-guided atom group around the
3258 z-axis by :math:`\theta` degress by using following input:
3259 :math:`(\cos \theta , -\sin \theta , 0 , \sin \theta , \cos \theta , 0 , 0 , 0 , 1)` .
3261 User defined thingies
3262 ^^^^^^^^^^^^^^^^^^^^^
3266 .. mdp:: userint1 (0)
3267 .. mdp:: userint2 (0)
3268 .. mdp:: userint3 (0)
3269 .. mdp:: userint4 (0)
3270 .. mdp:: userreal1 (0)
3271 .. mdp:: userreal2 (0)
3272 .. mdp:: userreal3 (0)
3273 .. mdp:: userreal4 (0)
3275 These you can use if you modify code. You can pass integers and
3276 reals and groups to your subroutine. Check the inputrec definition
3277 in ``src/gromacs/mdtypes/inputrec.h``
3282 These features have been removed from |Gromacs|, but so that old
3283 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3284 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3285 fatal error if this is set.
3291 .. mdp:: implicit-solvent
3295 .. _reference manual: gmx-manual-parent-dir_