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 :mdp:`nstlist`, unless
980 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
981 Verlet integrators :mdp:`nsttcouple` is set to 1.
983 .. mdp:: nh-chain-length
986 The number of chained Nose-Hoover thermostats for velocity Verlet
987 integrators, the leap-frog :mdp-value:`integrator=md` integrator
988 only supports 1. Data for the NH chain variables is not printed
989 to the :ref:`edr` file by default, but can be turned on with the
990 :mdp:`print-nose-hoover-chain-variables` option.
992 .. mdp:: print-nose-hoover-chain-variables
996 Do not store Nose-Hoover chain variables in the energy file.
1000 Store all positions and velocities of the Nose-Hoover chain
1005 groups to couple to separate temperature baths
1010 time constant for coupling (one for each group in
1011 :mdp:`tc-grps`), -1 means no temperature coupling
1016 reference temperature for coupling (one for each group in
1027 No pressure coupling. This means a fixed box size.
1029 .. mdp-value:: Berendsen
1031 Exponential relaxation pressure coupling with time constant
1032 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1033 argued that this does not yield a correct thermodynamic
1034 ensemble, but it is the most efficient way to scale a box at the
1037 .. mdp-value:: Parrinello-Rahman
1039 Extended-ensemble pressure coupling where the box vectors are
1040 subject to an equation of motion. The equation of motion for the
1041 atoms is coupled to this. No instantaneous scaling takes
1042 place. As for Nose-Hoover temperature coupling the time constant
1043 :mdp:`tau-p` is the period of pressure fluctuations at
1044 equilibrium. This is probably a better method when you want to
1045 apply pressure scaling during data collection, but beware that
1046 you can get very large oscillations if you are starting from a
1047 different pressure. For simulations where the exact fluctations
1048 of the NPT ensemble are important, or if the pressure coupling
1049 time is very short it may not be appropriate, as the previous
1050 time step pressure is used in some steps of the |Gromacs|
1051 implementation for the current time step pressure.
1055 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1056 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1057 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1058 time constant :mdp:`tau-p` is the period of pressure
1059 fluctuations at equilibrium. This is probably a better method
1060 when you want to apply pressure scaling during data collection,
1061 but beware that you can get very large oscillations if you are
1062 starting from a different pressure. Currently (as of version
1063 5.1), it only supports isotropic scaling, and only works without
1068 Specifies the kind of isotropy of the pressure coupling used. Each
1069 kind takes one or more values for :mdp:`compressibility` and
1070 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1072 .. mdp-value:: isotropic
1074 Isotropic pressure coupling with time constant
1075 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1076 :mdp:`ref-p` is required.
1078 .. mdp-value:: semiisotropic
1080 Pressure coupling which is isotropic in the ``x`` and ``y``
1081 direction, but different in the ``z`` direction. This can be
1082 useful for membrane simulations. Two values each for
1083 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1084 ``x/y`` and ``z`` directions respectively.
1086 .. mdp-value:: anisotropic
1088 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1089 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1090 respectively. When the off-diagonal compressibilities are set to
1091 zero, a rectangular box will stay rectangular. Beware that
1092 anisotropic scaling can lead to extreme deformation of the
1095 .. mdp-value:: surface-tension
1097 Surface tension coupling for surfaces parallel to the
1098 xy-plane. Uses normal pressure coupling for the ``z``-direction,
1099 while the surface tension is coupled to the ``x/y`` dimensions of
1100 the box. The first :mdp:`ref-p` value is the reference surface
1101 tension times the number of surfaces ``bar nm``, the second
1102 value is the reference ``z``-pressure ``bar``. The two
1103 :mdp:`compressibility` values are the compressibility in the
1104 ``x/y`` and ``z`` direction respectively. The value for the
1105 ``z``-compressibility should be reasonably accurate since it
1106 influences the convergence of the surface-tension, it can also
1107 be set to zero to have a box with constant height.
1112 The frequency for coupling the pressure. The default value of -1
1113 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1114 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1115 Verlet integrators :mdp:`nstpcouple` is set to 1.
1120 The time constant for pressure coupling (one value for all
1123 .. mdp:: compressibility
1126 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1127 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1128 required values is implied by :mdp:`pcoupltype`.
1133 The reference pressure for coupling. The number of required values
1134 is implied by :mdp:`pcoupltype`.
1136 .. mdp:: refcoord-scaling
1140 The reference coordinates for position restraints are not
1141 modified. Note that with this option the virial and pressure
1142 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1147 The reference coordinates are scaled with the scaling matrix of
1148 the pressure coupling.
1152 Scale the center of mass of the reference coordinates with the
1153 scaling matrix of the pressure coupling. The vectors of each
1154 reference coordinate to the center of mass are not scaled. Only
1155 one COM is used, even when there are multiple molecules with
1156 position restraints. For calculating the COM of the reference
1157 coordinates in the starting configuration, periodic boundary
1158 conditions are not taken into account. Note that with this option
1159 the virial and pressure might be ill defined, see
1160 :ref:`here <reference-manual-position-restraints>` for more details.
1166 Simulated annealing is controlled separately for each temperature
1167 group in |Gromacs|. The reference temperature is a piecewise linear
1168 function, but you can use an arbitrary number of points for each
1169 group, and choose either a single sequence or a periodic behaviour for
1170 each group. The actual annealing is performed by dynamically changing
1171 the reference temperature used in the thermostat algorithm selected,
1172 so remember that the system will usually not instantaneously reach the
1173 reference temperature!
1177 Type of annealing for each temperature group
1181 No simulated annealing - just couple to reference temperature value.
1183 .. mdp-value:: single
1185 A single sequence of annealing points. If your simulation is
1186 longer than the time of the last point, the temperature will be
1187 coupled to this constant value after the annealing sequence has
1188 reached the last time point.
1190 .. mdp-value:: periodic
1192 The annealing will start over at the first reference point once
1193 the last reference time is reached. This is repeated until the
1196 .. mdp:: annealing-npoints
1198 A list with the number of annealing reference/control points used
1199 for each temperature group. Use 0 for groups that are not
1200 annealed. The number of entries should equal the number of
1203 .. mdp:: annealing-time
1205 List of times at the annealing reference/control points for each
1206 group. If you are using periodic annealing, the times will be used
1207 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1208 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1209 etc. The number of entries should equal the sum of the numbers
1210 given in :mdp:`annealing-npoints`.
1212 .. mdp:: annealing-temp
1214 List of temperatures at the annealing reference/control points for
1215 each group. The number of entries should equal the sum of the
1216 numbers given in :mdp:`annealing-npoints`.
1218 Confused? OK, let's use an example. Assume you have two temperature
1219 groups, set the group selections to ``annealing = single periodic``,
1220 the number of points of each group to ``annealing-npoints = 3 4``, the
1221 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1222 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1223 will be coupled to 298K at 0ps, but the reference temperature will
1224 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1225 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1226 second group is coupled to 298K at 0ps, it increases linearly to 320K
1227 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1228 decreases to 298K, and then it starts over with the same pattern
1229 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1230 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1240 Do not generate velocities. The velocities are set to zero
1241 when there are no velocities in the input structure file.
1245 Generate velocities in :ref:`gmx grompp` according to a
1246 Maxwell distribution at temperature :mdp:`gen-temp`, with
1247 random seed :mdp:`gen-seed`. This is only meaningful with
1248 :mdp-value:`integrator=md`.
1253 temperature for Maxwell distribution
1258 used to initialize random generator for random velocities,
1259 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1266 .. mdp:: constraints
1268 Controls which bonds in the topology will be converted to rigid
1269 holonomic constraints. Note that typical rigid water models do not
1270 have bonds, but rather a specialized ``[settles]`` directive, so
1271 are not affected by this keyword.
1275 No bonds converted to constraints.
1277 .. mdp-value:: h-bonds
1279 Convert the bonds with H-atoms to constraints.
1281 .. mdp-value:: all-bonds
1283 Convert all bonds to constraints.
1285 .. mdp-value:: h-angles
1287 Convert all bonds to constraints and convert the angles that
1288 involve H-atoms to bond-constraints.
1290 .. mdp-value:: all-angles
1292 Convert all bonds to constraints and all angles to bond-constraints.
1294 .. mdp:: constraint-algorithm
1296 Chooses which solver satisfies any non-SETTLE holonomic
1299 .. mdp-value:: LINCS
1301 LINear Constraint Solver. With domain decomposition the parallel
1302 version P-LINCS is used. The accuracy in set with
1303 :mdp:`lincs-order`, which sets the number of matrices in the
1304 expansion for the matrix inversion. After the matrix inversion
1305 correction the algorithm does an iterative correction to
1306 compensate for lengthening due to rotation. The number of such
1307 iterations can be controlled with :mdp:`lincs-iter`. The root
1308 mean square relative constraint deviation is printed to the log
1309 file every :mdp:`nstlog` steps. If a bond rotates more than
1310 :mdp:`lincs-warnangle` in one step, a warning will be printed
1311 both to the log file and to ``stderr``. LINCS should not be used
1312 with coupled angle constraints.
1314 .. mdp-value:: SHAKE
1316 SHAKE is slightly slower and less stable than LINCS, but does
1317 work with angle constraints. The relative tolerance is set with
1318 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1319 does not support constraints between atoms on different
1320 decomposition domains, so it can only be used with domain
1321 decomposition when so-called update-groups are used, which is
1322 usally the case when only bonds involving hydrogens are
1323 constrained. SHAKE can not be used with energy minimization.
1325 .. mdp:: continuation
1327 This option was formerly known as ``unconstrained-start``.
1331 apply constraints to the start configuration and reset shells
1335 do not apply constraints to the start configuration and do not
1336 reset shells, useful for exact coninuation and reruns
1341 relative tolerance for SHAKE
1343 .. mdp:: lincs-order
1346 Highest order in the expansion of the constraint coupling
1347 matrix. When constraints form triangles, an additional expansion of
1348 the same order is applied on top of the normal expansion only for
1349 the couplings within such triangles. For "normal" MD simulations an
1350 order of 4 usually suffices, 6 is needed for large time-steps with
1351 virtual sites or BD. For accurate energy minimization an order of 8
1352 or more might be required. With domain decomposition, the cell size
1353 is limited by the distance spanned by :mdp:`lincs-order` +1
1354 constraints. When one wants to scale further than this limit, one
1355 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1356 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1357 )* :mdp:`lincs-order` remains constant.
1362 Number of iterations to correct for rotational lengthening in
1363 LINCS. For normal runs a single step is sufficient, but for NVE
1364 runs where you want to conserve energy accurately or for accurate
1365 energy minimization you might want to increase it to 2.
1367 .. mdp:: lincs-warnangle
1370 maximum angle that a bond can rotate before LINCS will complain
1376 bonds are represented by a harmonic potential
1380 bonds are represented by a Morse potential
1383 Energy group exclusions
1384 ^^^^^^^^^^^^^^^^^^^^^^^
1386 .. mdp:: energygrp-excl
1388 Pairs of energy groups for which all non-bonded interactions are
1389 excluded. An example: if you have two energy groups ``Protein`` and
1390 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1391 would give only the non-bonded interactions between the protein and
1392 the solvent. This is especially useful for speeding up energy
1393 calculations with ``mdrun -rerun`` and for excluding interactions
1394 within frozen groups.
1403 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1404 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1405 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1406 used (it is usually best to use semiisotropic pressure coupling
1407 with the ``x/y`` compressibility set to 0, as otherwise the surface
1408 area will change). Walls interact wit the rest of the system
1409 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1410 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1411 monitor the interaction of energy groups with each wall. The center
1412 of mass motion removal will be turned off in the ``z``-direction.
1414 .. mdp:: wall-atomtype
1416 the atom type name in the force field for each wall. By (for
1417 example) defining a special wall atom type in the topology with its
1418 own combination rules, this allows for independent tuning of the
1419 interaction of each atomtype with the walls.
1425 LJ integrated over the volume behind the wall: 9-3 potential
1429 LJ integrated over the wall surface: 10-4 potential
1433 direct LJ potential with the ``z`` distance from the wall
1437 user defined potentials indexed with the ``z`` distance from the
1438 wall, the tables are read analogously to the
1439 :mdp:`energygrp-table` option, where the first name is for a
1440 "normal" energy group and the second name is ``wall0`` or
1441 ``wall1``, only the dispersion and repulsion columns are used
1443 .. mdp:: wall-r-linpot
1446 Below this distance from the wall the potential is continued
1447 linearly and thus the force is constant. Setting this option to a
1448 postive value is especially useful for equilibration when some
1449 atoms are beyond a wall. When the value is <=0 (<0 for
1450 :mdp:`wall-type` =table), a fatal error is generated when atoms
1453 .. mdp:: wall-density
1455 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1456 the number density of the atoms for each wall for wall types 9-3
1459 .. mdp:: wall-ewald-zfac
1462 The scaling factor for the third box vector for Ewald summation
1463 only, the minimum is 2. Ewald summation can only be used with
1464 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1465 ``=3dc``. The empty layer in the box serves to decrease the
1466 unphysical Coulomb interaction between periodic images.
1472 Note that where pulling coordinates are applicable, there can be more
1473 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1474 variables will exist accordingly. Documentation references to things
1475 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1476 applicable pulling coordinate, eg. the second pull coordinate is described by
1477 pull-coord2-vec, pull-coord2-k, and so on.
1483 No center of mass pulling. All the following pull options will
1484 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1489 Center of mass pulling will be applied on 1 or more groups using
1490 1 or more pull coordinates.
1492 .. mdp:: pull-cylinder-r
1495 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1497 .. mdp:: pull-constr-tol
1500 the relative constraint tolerance for constraint pulling
1502 .. mdp:: pull-print-com
1506 do not print the COM for any group
1510 print the COM of all groups for all pull coordinates
1512 .. mdp:: pull-print-ref-value
1516 do not print the reference value for each pull coordinate
1520 print the reference value for each pull coordinate
1522 .. mdp:: pull-print-components
1526 only print the distance for each pull coordinate
1530 print the distance and Cartesian components selected in
1531 :mdp:`pull-coord1-dim`
1533 .. mdp:: pull-nstxout
1536 frequency for writing out the COMs of all the pull group (0 is
1539 .. mdp:: pull-nstfout
1542 frequency for writing out the force of all the pulled group
1545 .. mdp:: pull-pbc-ref-prev-step-com
1549 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1550 treatment of periodic boundary conditions.
1554 Use the COM of the previous step as reference for the treatment
1555 of periodic boundary conditions. The reference is initialized
1556 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1557 be located centrally in the group. Using the COM from the
1558 previous step can be useful if one or more pull groups are large.
1560 .. mdp:: pull-xout-average
1564 Write the instantaneous coordinates for all the pulled groups.
1568 Write the average coordinates (since last output) for all the
1569 pulled groups. N.b., some analysis tools might expect instantaneous
1572 .. mdp:: pull-fout-average
1576 Write the instantaneous force for all the pulled groups.
1580 Write the average force (since last output) for all the
1581 pulled groups. N.b., some analysis tools might expect instantaneous
1584 .. mdp:: pull-ngroups
1587 The number of pull groups, not including the absolute reference
1588 group, when used. Pull groups can be reused in multiple pull
1589 coordinates. Below only the pull options for group 1 are given,
1590 further groups simply increase the group index number.
1592 .. mdp:: pull-ncoords
1595 The number of pull coordinates. Below only the pull options for
1596 coordinate 1 are given, further coordinates simply increase the
1597 coordinate index number.
1599 .. mdp:: pull-group1-name
1601 The name of the pull group, is looked up in the index file or in
1602 the default groups to obtain the atoms involved.
1604 .. mdp:: pull-group1-weights
1606 Optional relative weights which are multiplied with the masses of
1607 the atoms to give the total weight for the COM. The number should
1608 be 0, meaning all 1, or the number of atoms in the pull group.
1610 .. mdp:: pull-group1-pbcatom
1613 The reference atom for the treatment of periodic boundary
1614 conditions inside the group (this has no effect on the treatment of
1615 the pbc between groups). This option is only important when the
1616 diameter of the pull group is larger than half the shortest box
1617 vector. For determining the COM, all atoms in the group are put at
1618 their periodic image which is closest to
1619 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1620 atom (number wise) is used, which is only safe for small groups.
1621 :ref:`gmx grompp` checks that the maximum distance from the reference
1622 atom (specifically chosen, or not) to the other atoms in the group
1623 is not too large. This parameter is not used with
1624 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1625 weighting, which is useful for a group of molecules in a periodic
1626 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1629 .. mdp:: pull-coord1-type
1631 .. mdp-value:: umbrella
1633 Center of mass pulling using an umbrella potential between the
1634 reference group and one or more groups.
1636 .. mdp-value:: constraint
1638 Center of mass pulling using a constraint between the reference
1639 group and one or more groups. The setup is identical to the
1640 option umbrella, except for the fact that a rigid constraint is
1641 applied instead of a harmonic potential.
1643 .. mdp-value:: constant-force
1645 Center of mass pulling using a linear potential and therefore a
1646 constant force. For this option there is no reference position
1647 and therefore the parameters :mdp:`pull-coord1-init` and
1648 :mdp:`pull-coord1-rate` are not used.
1650 .. mdp-value:: flat-bottom
1652 At distances above :mdp:`pull-coord1-init` a harmonic potential
1653 is applied, otherwise no potential is applied.
1655 .. mdp-value:: flat-bottom-high
1657 At distances below :mdp:`pull-coord1-init` a harmonic potential
1658 is applied, otherwise no potential is applied.
1660 .. mdp-value:: external-potential
1662 An external potential that needs to be provided by another
1665 .. mdp:: pull-coord1-potential-provider
1667 The name of the external module that provides the potential for
1668 the case where :mdp:`pull-coord1-type` is external-potential.
1670 .. mdp:: pull-coord1-geometry
1672 .. mdp-value:: distance
1674 Pull along the vector connecting the two groups. Components can
1675 be selected with :mdp:`pull-coord1-dim`.
1677 .. mdp-value:: direction
1679 Pull in the direction of :mdp:`pull-coord1-vec`.
1681 .. mdp-value:: direction-periodic
1683 As :mdp-value:`pull-coord1-geometry=direction`, but does not apply
1684 periodic box vector corrections to keep the distance within half
1685 the box length. This is (only) useful for pushing groups apart
1686 by more than half the box length by continuously changing the reference
1687 location using a pull rate. With this geometry the box should not be
1688 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1689 the pull force is not added to the virial.
1691 .. mdp-value:: direction-relative
1693 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1694 that points from the COM of a third to the COM of a fourth pull
1695 group. This means that 4 groups need to be supplied in
1696 :mdp:`pull-coord1-groups`. Note that the pull force will give
1697 rise to a torque on the pull vector, which is turn leads to
1698 forces perpendicular to the pull vector on the two groups
1699 defining the vector. If you want a pull group to move between
1700 the two groups defining the vector, simply use the union of
1701 these two groups as the reference group.
1703 .. mdp-value:: cylinder
1705 Designed for pulling with respect to a layer where the reference
1706 COM is given by a local cylindrical part of the reference group.
1707 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1708 the first of the two groups in :mdp:`pull-coord1-groups` a
1709 cylinder is selected around the axis going through the COM of
1710 the second group with direction :mdp:`pull-coord1-vec` with
1711 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1712 continously to zero as the radial distance goes from 0 to
1713 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1714 dependence gives rise to radial forces on both pull groups.
1715 Note that the radius should be smaller than half the box size.
1716 For tilted cylinders they should be even smaller than half the
1717 box size since the distance of an atom in the reference group
1718 from the COM of the pull group has both a radial and an axial
1719 component. This geometry is not supported with constraint
1722 .. mdp-value:: angle
1724 Pull along an angle defined by four groups. The angle is
1725 defined as the angle between two vectors: the vector connecting
1726 the COM of the first group to the COM of the second group and
1727 the vector connecting the COM of the third group to the COM of
1730 .. mdp-value:: angle-axis
1732 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1733 Thus, only the two groups that define the first vector need to be given.
1735 .. mdp-value:: dihedral
1737 Pull along a dihedral angle defined by six groups. These pairwise
1738 define three vectors: the vector connecting the COM of group 1
1739 to the COM of group 2, the COM of group 3 to the COM of group 4,
1740 and the COM of group 5 to the COM group 6. The dihedral angle is
1741 then defined as the angle between two planes: the plane spanned by the
1742 the two first vectors and the plane spanned the two last vectors.
1745 .. mdp:: pull-coord1-groups
1747 The group indices on which this pull coordinate will operate.
1748 The number of group indices required is geometry dependent.
1749 The first index can be 0, in which case an
1750 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1751 absolute reference the system is no longer translation invariant
1752 and one should think about what to do with the center of mass
1755 .. mdp:: pull-coord1-dim
1758 Selects the dimensions that this pull coordinate acts on and that
1759 are printed to the output files when
1760 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1761 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1762 components set to Y contribute to the distance. Thus setting this
1763 to Y Y N results in a distance in the x/y plane. With other
1764 geometries all dimensions with non-zero entries in
1765 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1766 dimensions only affect the output.
1768 .. mdp:: pull-coord1-origin
1771 The pull reference position for use with an absolute reference.
1773 .. mdp:: pull-coord1-vec
1776 The pull direction. :ref:`gmx grompp` normalizes the vector.
1778 .. mdp:: pull-coord1-start
1782 do not modify :mdp:`pull-coord1-init`
1786 add the COM distance of the starting conformation to
1787 :mdp:`pull-coord1-init`
1789 .. mdp:: pull-coord1-init
1792 The reference distance or reference angle at t=0.
1794 .. mdp:: pull-coord1-rate
1796 (0) [nm/ps] or [deg/ps]
1797 The rate of change of the reference position or reference angle.
1799 .. mdp:: pull-coord1-k
1801 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1802 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1803 The force constant. For umbrella pulling this is the harmonic force
1804 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1805 for angles). For constant force pulling this is the
1806 force constant of the linear potential, and thus the negative (!)
1807 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1808 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1809 Note that for angles the force constant is expressed in terms of radians
1810 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1812 .. mdp:: pull-coord1-kB
1814 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1815 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1816 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1817 :mdp:`free-energy` is turned on. The force constant is then (1 -
1818 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1820 AWH adaptive biasing
1821 ^^^^^^^^^^^^^^^^^^^^
1831 Adaptively bias a reaction coordinate using the AWH method and estimate
1832 the corresponding PMF. The PMF and other AWH data are written to energy
1833 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1834 the ``gmx awh`` tool. The AWH coordinate can be
1835 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1836 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1837 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1838 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1840 .. mdp:: awh-potential
1842 .. mdp-value:: convolved
1844 The applied biasing potential is the convolution of the bias function and a
1845 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1846 in a smooth potential function and force. The resolution of the potential is set
1847 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1849 .. mdp-value:: umbrella
1851 The potential bias is applied by controlling the position of an harmonic potential
1852 using Monte-Carlo sampling. The force constant is set with
1853 :mdp:`awh1-dim1-force-constant`. The umbrella location
1854 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1855 There are no advantages to using an umbrella.
1856 This option is mainly for comparison and testing purposes.
1858 .. mdp:: awh-share-multisim
1862 AWH will not share biases across simulations started with
1863 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1867 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1868 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1869 with the biases with the same :mdp:`awh1-share-group` value.
1870 The simulations should have the same AWH settings for sharing to make sense.
1871 :ref:`gmx mdrun` will check whether the simulations are technically
1872 compatible for sharing, but the user should check that bias sharing
1873 physically makes sense.
1877 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1878 where -1 indicates to generate a seed. Only used with
1879 :mdp-value:`awh-potential=umbrella`.
1884 Number of steps between printing AWH data to the energy file, should be
1885 a multiple of :mdp:`nstenergy`.
1887 .. mdp:: awh-nstsample
1890 Number of steps between sampling of the coordinate value. This sampling
1891 is the basis for updating the bias and estimating the PMF and other AWH observables.
1893 .. mdp:: awh-nsamples-update
1896 The number of coordinate samples used for each AWH update.
1897 The update interval in steps is :mdp:`awh-nstsample` times this value.
1902 The number of biases, each acting on its own coordinate.
1903 The following options should be specified
1904 for each bias although below only the options for bias number 1 is shown. Options for
1905 other bias indices are obtained by replacing '1' by the bias index.
1907 .. mdp:: awh1-error-init
1909 (10.0) [kJ mol\ :sup:`-1`]
1910 Estimated initial average error of the PMF for this bias. This value together with the
1911 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1912 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1914 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1915 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1916 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1917 then :mdp:`awh1-error-init` should reflect that knowledge.
1919 .. mdp:: awh1-growth
1921 .. mdp-value:: exp-linear
1923 Each bias keeps a reference weight histogram for the coordinate samples.
1924 Its size sets the magnitude of the bias function and free energy estimate updates
1925 (few samples corresponds to large updates and vice versa).
1926 Thus, its growth rate sets the maximum convergence rate.
1927 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1928 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1929 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1930 high free energy barriers have not yet been flattened by the bias.
1932 .. mdp-value:: linear
1934 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1935 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
1936 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
1938 .. mdp:: awh1-equilibrate-histogram
1942 Do not equilibrate histogram.
1946 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
1947 histogram of sampled weights is following the target distribution closely enough (specifically,
1948 at least 80% of the target region needs to have a local relative error of less than 20%). This
1949 option would typically only be used when :mdp:`awh1-share-group` > 0
1950 and the initial configurations poorly represent the target
1953 .. mdp:: awh1-target
1955 .. mdp-value:: constant
1957 The bias is tuned towards a constant (uniform) coordinate distribution
1958 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
1960 .. mdp-value:: cutoff
1962 Similar to :mdp-value:`awh1-target=constant`, but the target
1963 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
1964 where F is the free energy relative to the estimated global minimum.
1965 This provides a smooth switch of a flat target distribution in
1966 regions with free energy lower than the cut-off to a Boltzmann
1967 distribution in regions with free energy higher than the cut-off.
1969 .. mdp-value:: boltzmann
1971 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
1972 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
1973 would give the same coordinate distribution as sampling with a simulation temperature
1976 .. mdp-value:: local-boltzmann
1978 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
1979 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
1980 change of the bias only depends on the local sampling. This local convergence property is
1981 only compatible with :mdp-value:`awh1-growth=linear`, since for
1982 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
1984 .. mdp:: awh1-target-beta-scaling
1987 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
1988 it is the unitless beta scaling factor taking values in (0,1).
1990 .. mdp:: awh1-target-cutoff
1992 (0) [kJ mol\ :sup:`-1`]
1993 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
1995 .. mdp:: awh1-user-data
1999 Initialize the PMF and target distribution with default values.
2003 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2004 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2005 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2006 The file name can be changed with the ``-awh`` option.
2007 The first :mdp:`awh1-ndim` columns of
2008 each input file should contain the coordinate values, such that each row defines a point in
2009 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
2010 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2011 be in the same column as written by :ref:`gmx awh`.
2013 .. mdp:: awh1-share-group
2017 Do not share the bias.
2019 .. mdp-value:: positive
2021 Share the bias and PMF estimates within and/or between simulations.
2022 Within a simulation, the bias will be shared between biases that have the
2023 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2024 With :mdp-value:`awh-share-multisim=yes` and
2025 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2026 Sharing may increase convergence initially, although the starting configurations
2027 can be critical, especially when sharing between many biases.
2028 Currently, positive group values should start at 1 and increase
2029 by 1 for each subsequent bias that is shared.
2034 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2035 The following options should be specified for each such dimension. Below only
2036 the options for dimension number 1 is shown. Options for other dimension indices are
2037 obtained by replacing '1' by the dimension index.
2039 .. mdp:: awh1-dim1-coord-provider
2043 The module providing the reaction coordinate for this dimension.
2044 Currently AWH can only act on pull coordinates.
2046 .. mdp:: awh1-dim1-coord-index
2049 Index of the pull coordinate defining this coordinate dimension.
2051 .. mdp:: awh1-dim1-force-constant
2053 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2054 Force constant for the (convolved) umbrella potential(s) along this
2055 coordinate dimension.
2057 .. mdp:: awh1-dim1-start
2060 Start value of the sampling interval along this dimension. The range of allowed
2061 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2062 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2063 is allowed. The interval will then wrap around from +period/2 to -period/2.
2064 For the direction geometry, the dimension is made periodic when
2065 the direction is along a box vector and covers more than 95%
2066 of the box length. Note that one should not apply pressure coupling
2067 along a periodic dimension.
2069 .. mdp:: awh1-dim1-end
2072 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2074 .. mdp:: awh1-dim1-diffusion
2076 (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps]
2077 Estimated diffusion constant for this coordinate dimension determining the initial
2078 biasing rate. This needs only be a rough estimate and should not critically
2079 affect the results unless it is set to something very low, leading to slow convergence,
2080 or very high, forcing the system far from equilibrium. Not setting this value
2081 explicitly generates a warning.
2083 .. mdp:: awh1-dim1-cover-diameter
2086 Diameter that needs to be sampled by a single simulation around a coordinate value
2087 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2088 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2089 across each coordinate value.
2090 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2091 (:mdp:`awh1-share-group`>0).
2092 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2093 for many sharing simulations does not guarantee transitions across free energy barriers.
2094 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2095 has independently sampled the whole interval.
2100 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2101 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2102 that can be used to achieve such a rotation.
2108 No enforced rotation will be applied. All enforced rotation options will
2109 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2114 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2115 under the :mdp:`rot-group0` option.
2117 .. mdp:: rot-ngroups
2120 Number of rotation groups.
2124 Name of rotation group 0 in the index file.
2129 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2130 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2131 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2136 Use mass weighted rotation group positions.
2141 Rotation vector, will get normalized.
2146 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2150 (0) [degree ps\ :sup:`-1`]
2151 Reference rotation rate of group 0.
2155 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2156 Force constant for group 0.
2158 .. mdp:: rot-slab-dist0
2161 Slab distance, if a flexible axis rotation type was chosen.
2163 .. mdp:: rot-min-gauss0
2166 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2167 (for the flexible axis potentials).
2171 (0.0001) [nm\ :sup:`2`]
2172 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2174 .. mdp:: rot-fit-method0
2177 Fitting method when determining the actual angle of a rotation group
2178 (can be one of ``rmsd``, ``norm``, or ``potential``).
2180 .. mdp:: rot-potfit-nsteps0
2183 For fit type ``potential``, the number of angular positions around the reference angle for which the
2184 rotation potential is evaluated.
2186 .. mdp:: rot-potfit-step0
2189 For fit type ``potential``, the distance in degrees between two angular positions.
2191 .. mdp:: rot-nstrout
2194 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2195 and the rotation potential energy.
2197 .. mdp:: rot-nstsout
2200 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2210 ignore distance restraint information in topology file
2212 .. mdp-value:: simple
2214 simple (per-molecule) distance restraints.
2216 .. mdp-value:: ensemble
2218 distance restraints over an ensemble of molecules in one
2219 simulation box. Normally, one would perform ensemble averaging
2220 over multiple simulations, using ``mdrun
2221 -multidir``. The environment
2222 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2223 within each ensemble (usually equal to the number of directories
2224 supplied to ``mdrun -multidir``).
2226 .. mdp:: disre-weighting
2228 .. mdp-value:: equal
2230 divide the restraint force equally over all atom pairs in the
2233 .. mdp-value:: conservative
2235 the forces are the derivative of the restraint potential, this
2236 results in an weighting of the atom pairs to the reciprocal
2237 seventh power of the displacement. The forces are conservative
2238 when :mdp:`disre-tau` is zero.
2240 .. mdp:: disre-mixed
2244 the violation used in the calculation of the restraint force is
2245 the time-averaged violation
2249 the violation used in the calculation of the restraint force is
2250 the square root of the product of the time-averaged violation
2251 and the instantaneous violation
2255 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2256 force constant for distance restraints, which is multiplied by a
2257 (possibly) different factor for each restraint given in the ``fac``
2258 column of the interaction in the topology file.
2263 time constant for distance restraints running average. A value of
2264 zero turns off time averaging.
2266 .. mdp:: nstdisreout
2269 period between steps when the running time-averaged and
2270 instantaneous distances of all atom pairs involved in restraints
2271 are written to the energy file (can make the energy file very
2278 ignore orientation restraint information in topology file
2282 use orientation restraints, ensemble averaging can be performed
2283 with ``mdrun -multidir``
2287 (0) [kJ mol\ :sup:`-1`]
2288 force constant for orientation restraints, which is multiplied by a
2289 (possibly) different weight factor for each restraint, can be set
2290 to zero to obtain the orientations from a free simulation
2295 time constant for orientation restraints running average. A value
2296 of zero turns off time averaging.
2298 .. mdp:: orire-fitgrp
2300 fit group for orientation restraining. This group of atoms is used
2301 to determine the rotation **R** of the system with respect to the
2302 reference orientation. The reference orientation is the starting
2303 conformation of the first subsystem. For a protein, backbone is a
2306 .. mdp:: nstorireout
2309 period between steps when the running time-averaged and
2310 instantaneous orientations for all restraints, and the molecular
2311 order tensor are written to the energy file (can make the energy
2315 Free energy calculations
2316 ^^^^^^^^^^^^^^^^^^^^^^^^
2318 .. mdp:: free-energy
2322 Only use topology A.
2326 Interpolate between topology A (lambda=0) to topology B
2327 (lambda=1) and write the derivative of the Hamiltonian with
2328 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2329 or the Hamiltonian differences with respect to other lambda
2330 values (as specified with foreign lambda) to the energy file
2331 and/or to ``dhdl.xvg``, where they can be processed by, for
2332 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2333 are interpolated linearly as described in the manual. When
2334 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2335 used for the LJ and Coulomb interactions.
2339 Turns on expanded ensemble simulation, where the alchemical state
2340 becomes a dynamic variable, allowing jumping between different
2341 Hamiltonians. See the expanded ensemble options for controlling how
2342 expanded ensemble simulations are performed. The different
2343 Hamiltonians used in expanded ensemble simulations are defined by
2344 the other free energy options.
2346 .. mdp:: init-lambda
2349 starting value for lambda (float). Generally, this should only be
2350 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2351 other cases, :mdp:`init-lambda-state` should be specified
2352 instead. Must be greater than or equal to 0.
2354 .. mdp:: delta-lambda
2357 increment per time step for lambda
2359 .. mdp:: init-lambda-state
2362 starting value for the lambda state (integer). Specifies which
2363 columm of the lambda vector (:mdp:`coul-lambdas`,
2364 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2365 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2366 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2367 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2368 the first column, and so on.
2370 .. mdp:: fep-lambdas
2373 Zero, one or more lambda values for which Delta H values will be
2374 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2375 steps. Values must be between 0 and 1. Free energy differences
2376 between different lambda values can then be determined with
2377 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2378 other -lambdas keywords because all components of the lambda vector
2379 that are not specified will use :mdp:`fep-lambdas` (including
2380 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2382 .. mdp:: coul-lambdas
2385 Zero, one or more lambda values for which Delta H values will be
2386 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2387 steps. Values must be between 0 and 1. Only the electrostatic
2388 interactions are controlled with this component of the lambda
2389 vector (and only if the lambda=0 and lambda=1 states have differing
2390 electrostatic interactions).
2392 .. mdp:: vdw-lambdas
2395 Zero, one or more lambda values for which Delta H values will be
2396 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2397 steps. Values must be between 0 and 1. Only the van der Waals
2398 interactions are controlled with this component of the lambda
2401 .. mdp:: bonded-lambdas
2404 Zero, one or more lambda values for which Delta H values will be
2405 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2406 steps. Values must be between 0 and 1. Only the bonded interactions
2407 are controlled with this component of the lambda vector.
2409 .. mdp:: restraint-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 restraint
2415 interactions: dihedral restraints, and the pull code restraints are
2416 controlled with this component of the lambda vector.
2418 .. mdp:: mass-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 particle masses are
2424 controlled with this component of the lambda vector.
2426 .. mdp:: temperature-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 temperatures
2432 controlled with this component of the lambda vector. Note that
2433 these lambdas should not be used for replica exchange, only for
2434 simulated tempering.
2436 .. mdp:: calc-lambda-neighbors
2439 Controls the number of lambda values for which Delta H values will
2440 be calculated and written out, if :mdp:`init-lambda-state` has
2441 been set. A positive value will limit the number of lambda points
2442 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2443 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2444 has a value of 2, energies for lambda points 3-7 will be calculated
2445 and writen out. A value of -1 means all lambda points will be
2446 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2447 1 is sufficient, while for MBAR -1 should be used.
2452 the soft-core alpha parameter, a value of 0 results in linear
2453 interpolation of the LJ and Coulomb interactions
2458 power 6 for the radial term in the soft-core equation.
2461 (deprecated) power 48 for the radial term in the soft-core equation.
2462 Note that sc-alpha should generally be much lower (between 0.001 and 0.003).
2467 Whether to apply the soft-core free energy interaction
2468 transformation to the Columbic interaction of a molecule. Default
2469 is no, as it is generally more efficient to turn off the Coulomic
2470 interactions linearly before turning off the van der Waals
2471 interactions. Note that it is only taken into account when lambda
2472 states are used, not with :mdp:`couple-lambda0` /
2473 :mdp:`couple-lambda1`, and you can still turn off soft-core
2474 interactions by setting :mdp:`sc-alpha` to 0.
2479 the power for lambda in the soft-core function, only the values 1
2485 the soft-core sigma for particles which have a C6 or C12 parameter
2486 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2488 .. mdp:: couple-moltype
2490 Here one can supply a molecule type (as defined in the topology)
2491 for calculating solvation or coupling free energies. There is a
2492 special option ``system`` that couples all molecule types in the
2493 system. This can be useful for equilibrating a system starting from
2494 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2495 on. The Van der Waals interactions and/or charges in this molecule
2496 type can be turned on or off between lambda=0 and lambda=1,
2497 depending on the settings of :mdp:`couple-lambda0` and
2498 :mdp:`couple-lambda1`. If you want to decouple one of several
2499 copies of a molecule, you need to copy and rename the molecule
2500 definition in the topology.
2502 .. mdp:: couple-lambda0
2504 .. mdp-value:: vdw-q
2506 all interactions are on at lambda=0
2510 the charges are zero (no Coulomb interactions) at lambda=0
2514 the Van der Waals interactions are turned at lambda=0; soft-core
2515 interactions will be required to avoid singularities
2519 the Van der Waals interactions are turned off and the charges
2520 are zero at lambda=0; soft-core interactions will be required to
2521 avoid singularities.
2523 .. mdp:: couple-lambda1
2525 analogous to :mdp:`couple-lambda1`, but for lambda=1
2527 .. mdp:: couple-intramol
2531 All intra-molecular non-bonded interactions for moleculetype
2532 :mdp:`couple-moltype` are replaced by exclusions and explicit
2533 pair interactions. In this manner the decoupled state of the
2534 molecule corresponds to the proper vacuum state without
2535 periodicity effects.
2539 The intra-molecular Van der Waals and Coulomb interactions are
2540 also turned on/off. This can be useful for partitioning
2541 free-energies of relatively large molecules, where the
2542 intra-molecular non-bonded interactions might lead to
2543 kinetically trapped vacuum conformations. The 1-4 pair
2544 interactions are not turned off.
2549 the frequency for writing dH/dlambda and possibly Delta H to
2550 dhdl.xvg, 0 means no ouput, should be a multiple of
2551 :mdp:`nstcalcenergy`.
2553 .. mdp:: dhdl-derivatives
2557 If yes (the default), the derivatives of the Hamiltonian with
2558 respect to lambda at each :mdp:`nstdhdl` step are written
2559 out. These values are needed for interpolation of linear energy
2560 differences with :ref:`gmx bar` (although the same can also be
2561 achieved with the right foreign lambda setting, that may not be as
2562 flexible), or with thermodynamic integration
2564 .. mdp:: dhdl-print-energy
2568 Include either the total or the potential energy in the dhdl
2569 file. Options are 'no', 'potential', or 'total'. This information
2570 is needed for later free energy analysis if the states of interest
2571 are at different temperatures. If all states are at the same
2572 temperature, this information is not needed. 'potential' is useful
2573 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2574 file. When rerunning from an existing trajectory, the kinetic
2575 energy will often not be correct, and thus one must compute the
2576 residual free energy from the potential alone, with the kinetic
2577 energy component computed analytically.
2579 .. mdp:: separate-dhdl-file
2583 The free energy values that are calculated (as specified with
2584 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2585 written out to a separate file, with the default name
2586 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2591 The free energy values are written out to the energy output file
2592 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2593 steps), where they can be extracted with :ref:`gmx energy` or
2594 used directly with :ref:`gmx bar`.
2596 .. mdp:: dh-hist-size
2599 If nonzero, specifies the size of the histogram into which the
2600 Delta H values (specified with foreign lambda) and the derivative
2601 dH/dl values are binned, and written to ener.edr. This can be used
2602 to save disk space while calculating free energy differences. One
2603 histogram gets written for each foreign lambda and two for the
2604 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2605 histogram settings (too small size or too wide bins) can introduce
2606 errors. Do not use histograms unless you're certain you need it.
2608 .. mdp:: dh-hist-spacing
2611 Specifies the bin width of the histograms, in energy units. Used in
2612 conjunction with :mdp:`dh-hist-size`. This size limits the
2613 accuracy with which free energies can be calculated. Do not use
2614 histograms unless you're certain you need it.
2617 Expanded Ensemble calculations
2618 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2620 .. mdp:: nstexpanded
2622 The number of integration steps beween attempted moves changing the
2623 system Hamiltonian in expanded ensemble simulations. Must be a
2624 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2631 No Monte Carlo in state space is performed.
2633 .. mdp-value:: metropolis-transition
2635 Uses the Metropolis weights to update the expanded ensemble
2636 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2639 .. mdp-value:: barker-transition
2641 Uses the Barker transition critera to update the expanded
2642 ensemble weight of each state i, defined by exp(-beta_new
2643 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2645 .. mdp-value:: wang-landau
2647 Uses the Wang-Landau algorithm (in state space, not energy
2648 space) to update the expanded ensemble weights.
2650 .. mdp-value:: min-variance
2652 Uses the minimum variance updating method of Escobedo et al. to
2653 update the expanded ensemble weights. Weights will not be the
2654 free energies, but will rather emphasize states that need more
2655 sampling to give even uncertainty.
2657 .. mdp:: lmc-mc-move
2661 No Monte Carlo in state space is performed.
2663 .. mdp-value:: metropolis-transition
2665 Randomly chooses a new state up or down, then uses the
2666 Metropolis critera to decide whether to accept or reject:
2667 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2669 .. mdp-value:: barker-transition
2671 Randomly chooses a new state up or down, then uses the Barker
2672 transition critera to decide whether to accept or reject:
2673 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2675 .. mdp-value:: gibbs
2677 Uses the conditional weights of the state given the coordinate
2678 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2681 .. mdp-value:: metropolized-gibbs
2683 Uses the conditional weights of the state given the coordinate
2684 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2685 to move to, EXCLUDING the current state, then uses a rejection
2686 step to ensure detailed balance. Always more efficient that
2687 Gibbs, though only marginally so in many situations, such as
2688 when only the nearest neighbors have decent phase space
2694 random seed to use for Monte Carlo moves in state space. When
2695 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2697 .. mdp:: mc-temperature
2699 Temperature used for acceptance/rejection for Monte Carlo moves. If
2700 not specified, the temperature of the simulation specified in the
2701 first group of :mdp:`ref-t` is used.
2706 The cutoff for the histogram of state occupancies to be reset, and
2707 the free energy incrementor to be changed from delta to delta *
2708 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2709 each histogram) / (average number of samples at each
2710 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2711 histogram is only considered flat if all Nratio > 0.8 AND
2712 simultaneously all 1/Nratio > 0.8.
2717 Each time the histogram is considered flat, then the current value
2718 of the Wang-Landau incrementor for the free energies is multiplied
2719 by :mdp:`wl-scale`. Value must be between 0 and 1.
2721 .. mdp:: init-wl-delta
2724 The initial value of the Wang-Landau incrementor in kT. Some value
2725 near 1 kT is usually most efficient, though sometimes a value of
2726 2-3 in units of kT works better if the free energy differences are
2729 .. mdp:: wl-oneovert
2732 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2733 the large sample limit. There is significant evidence that the
2734 standard Wang-Landau algorithms in state space presented here
2735 result in free energies getting 'burned in' to incorrect values
2736 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2737 then when the incrementor becomes less than 1/N, where N is the
2738 mumber of samples collected (and thus proportional to the data
2739 collection time, hence '1 over t'), then the Wang-Lambda
2740 incrementor is set to 1/N, decreasing every step. Once this occurs,
2741 :mdp:`wl-ratio` is ignored, but the weights will still stop
2742 updating when the equilibration criteria set in
2743 :mdp:`lmc-weights-equil` is achieved.
2745 .. mdp:: lmc-repeats
2748 Controls the number of times that each Monte Carlo swap type is
2749 performed each iteration. In the limit of large numbers of Monte
2750 Carlo repeats, then all methods converge to Gibbs sampling. The
2751 value will generally not need to be different from 1.
2753 .. mdp:: lmc-gibbsdelta
2756 Limit Gibbs sampling to selected numbers of neighboring states. For
2757 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2758 sampling over all of the states that are defined. A positive value
2759 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2760 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2761 value of -1 means that all states are considered. For less than 100
2762 states, it is probably not that expensive to include all states.
2764 .. mdp:: lmc-forced-nstart
2767 Force initial state space sampling to generate weights. In order to
2768 come up with reasonable initial weights, this setting allows the
2769 simulation to drive from the initial to the final lambda state,
2770 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2771 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2772 sufficiently long (thousands of steps, perhaps), then the weights
2773 will be close to correct. However, in most cases, it is probably
2774 better to simply run the standard weight equilibration algorithms.
2776 .. mdp:: nst-transition-matrix
2779 Frequency of outputting the expanded ensemble transition matrix. A
2780 negative number means it will only be printed at the end of the
2783 .. mdp:: symmetrized-transition-matrix
2786 Whether to symmetrize the empirical transition matrix. In the
2787 infinite limit the matrix will be symmetric, but will diverge with
2788 statistical noise for short timescales. Forced symmetrization, by
2789 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2790 like the existence of (small magnitude) negative eigenvalues.
2792 .. mdp:: mininum-var-min
2795 The min-variance strategy (option of :mdp:`lmc-stats` is only
2796 valid for larger number of samples, and can get stuck if too few
2797 samples are used at each state. :mdp:`mininum-var-min` is the
2798 minimum number of samples that each state that are allowed before
2799 the min-variance strategy is activated if selected.
2801 .. mdp:: init-lambda-weights
2803 The initial weights (free energies) used for the expanded ensemble
2804 states. Default is a vector of zero weights. format is similar to
2805 the lambda vector settings in :mdp:`fep-lambdas`, except the
2806 weights can be any floating point number. Units are kT. Its length
2807 must match the lambda vector lengths.
2809 .. mdp:: lmc-weights-equil
2813 Expanded ensemble weights continue to be updated throughout the
2818 The input expanded ensemble weights are treated as equilibrated,
2819 and are not updated throughout the simulation.
2821 .. mdp-value:: wl-delta
2823 Expanded ensemble weight updating is stopped when the
2824 Wang-Landau incrementor falls below this value.
2826 .. mdp-value:: number-all-lambda
2828 Expanded ensemble weight updating is stopped when the number of
2829 samples at all of the lambda states is greater than this value.
2831 .. mdp-value:: number-steps
2833 Expanded ensemble weight updating is stopped when the number of
2834 steps is greater than the level specified by this value.
2836 .. mdp-value:: number-samples
2838 Expanded ensemble weight updating is stopped when the number of
2839 total samples across all lambda states is greater than the level
2840 specified by this value.
2842 .. mdp-value:: count-ratio
2844 Expanded ensemble weight updating is stopped when the ratio of
2845 samples at the least sampled lambda state and most sampled
2846 lambda state greater than this value.
2848 .. mdp:: simulated-tempering
2851 Turn simulated tempering on or off. Simulated tempering is
2852 implemented as expanded ensemble sampling with different
2853 temperatures instead of different Hamiltonians.
2855 .. mdp:: sim-temp-low
2858 Low temperature for simulated tempering.
2860 .. mdp:: sim-temp-high
2863 High temperature for simulated tempering.
2865 .. mdp:: simulated-tempering-scaling
2867 Controls the way that the temperatures at intermediate lambdas are
2868 calculated from the :mdp:`temperature-lambdas` part of the lambda
2871 .. mdp-value:: linear
2873 Linearly interpolates the temperatures using the values of
2874 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2875 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2876 a temperature of 350. A nonlinear set of temperatures can always
2877 be implemented with uneven spacing in lambda.
2879 .. mdp-value:: geometric
2881 Interpolates temperatures geometrically between
2882 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2883 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2884 :mdp:`sim-temp-low`) raised to the power of
2885 (i/(ntemps-1)). This should give roughly equal exchange for
2886 constant heat capacity, though of course things simulations that
2887 involve protein folding have very high heat capacity peaks.
2889 .. mdp-value:: exponential
2891 Interpolates temperatures exponentially between
2892 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2893 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2894 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2895 (i))-1)/(exp(1.0)-i)).
2903 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2904 in groups Protein and Sol will experience constant acceleration as
2905 specified in the :mdp:`accelerate` line
2909 (0) [nm ps\ :sup:`-2`]
2910 acceleration for :mdp:`acc-grps`; x, y and z for each group
2911 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2912 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
2917 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2918 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2919 specifies for which dimension(s) the freezing applies. To avoid
2920 spurious contributions to the virial and pressure due to large
2921 forces between completely frozen atoms you need to use energy group
2922 exclusions, this also saves computing time. Note that coordinates
2923 of frozen atoms are not scaled by pressure-coupling algorithms.
2927 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2928 specify ``Y`` or ``N`` for X, Y and Z and for each group (*e.g.*
2929 ``Y Y N N N N`` means that particles in the first group can move only in
2930 Z direction. The particles in the second group can move in any
2933 .. mdp:: cos-acceleration
2935 (0) [nm ps\ :sup:`-2`]
2936 the amplitude of the acceleration profile for calculating the
2937 viscosity. The acceleration is in the X-direction and the magnitude
2938 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2939 added to the energy file: the amplitude of the velocity profile and
2944 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
2945 The velocities of deformation for the box elements: a(x) b(y) c(z)
2946 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2947 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2948 elements are corrected for periodicity. The coordinates are
2949 transformed accordingly. Frozen degrees of freedom are (purposely)
2950 also transformed. The time ts is set to t at the first step and at
2951 steps at which x and v are written to trajectory to ensure exact
2952 restarts. Deformation can be used together with semiisotropic or
2953 anisotropic pressure coupling when the appropriate
2954 compressibilities are set to zero. The diagonal elements can be
2955 used to strain a solid. The off-diagonal elements can be used to
2956 shear a solid or a liquid.
2962 .. mdp:: electric-field-x
2963 .. mdp:: electric-field-y
2964 .. mdp:: electric-field-z
2966 Here you can specify an electric field that optionally can be
2967 alternating and pulsed. The general expression for the field
2968 has the form of a gaussian laser pulse:
2970 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
2972 For example, the four parameters for direction x are set in the
2973 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
2974 and ``electric-field-z``) like
2976 ``electric-field-x = E0 omega t0 sigma``
2978 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
2980 In the special case that ``sigma = 0``, the exponential term is omitted
2981 and only the cosine term is used. If also ``omega = 0`` a static
2982 electric field is applied.
2984 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
2987 Mixed quantum/classical molecular dynamics
2988 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2998 Do a QM/MM simulation. Several groups can be described at
2999 different QM levels separately. These are specified in the
3000 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
3001 initio* theory at which the groups are described is specified by
3002 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
3003 groups at different levels of theory is only possible with the
3004 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
3008 groups to be descibed at the QM level (works also in case of MiMiC QM/MM)
3012 .. mdp-value:: normal
3014 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
3015 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
3016 *ab initio* theory. The rest of the system is described at the
3017 MM level. The QM and MM subsystems interact as follows: MM point
3018 charges are included in the QM one-electron hamiltonian and all
3019 Lennard-Jones interactions are described at the MM level.
3021 .. mdp-value:: ONIOM
3023 The interaction between the subsystem is described using the
3024 ONIOM method by Morokuma and co-workers. There can be more than
3025 one :mdp:`QMMM-grps` each modeled at a different level of QM
3026 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
3031 Method used to compute the energy and gradients on the QM
3032 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
3033 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
3034 included in the active space is specified by :mdp:`CASelectrons`
3035 and :mdp:`CASorbitals`.
3040 Basis set used to expand the electronic wavefuntion. Only Gaussian
3041 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3042 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
3047 The total charge in ``e`` of the :mdp:`QMMM-grps`. In case there are
3048 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
3049 layer needs to be specified separately.
3054 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
3055 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
3056 needs to be specified separately.
3058 .. mdp:: CASorbitals
3061 The number of orbitals to be included in the active space when
3062 doing a CASSCF computation.
3064 .. mdp:: CASelectrons
3067 The number of electrons to be included in the active space when
3068 doing a CASSCF computation.
3074 No surface hopping. The system is always in the electronic
3079 Do a QM/MM MD simulation on the excited state-potential energy
3080 surface and enforce a *diabatic* hop to the ground-state when
3081 the system hits the conical intersection hyperline in the course
3082 the simulation. This option only works in combination with the
3086 Computational Electrophysiology
3087 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3088 Use these options to switch on and control ion/water position exchanges in "Computational
3089 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3095 Do not enable ion/water position exchanges.
3097 .. mdp-value:: X ; Y ; Z
3099 Allow for ion/water position exchanges along the chosen direction.
3100 In a typical setup with the membranes parallel to the x-y plane,
3101 ion/water pairs need to be exchanged in Z direction to sustain the
3102 requested ion concentrations in the compartments.
3104 .. mdp:: swap-frequency
3106 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3107 per compartment are determined and exchanges made if necessary.
3108 Normally it is not necessary to check at every time step.
3109 For typical Computational Electrophysiology setups, a value of about 100 is
3110 sufficient and yields a negligible performance impact.
3112 .. mdp:: split-group0
3114 Name of the index group of the membrane-embedded part of channel #0.
3115 The center of mass of these atoms defines one of the compartment boundaries
3116 and should be chosen such that it is near the center of the membrane.
3118 .. mdp:: split-group1
3120 Channel #1 defines the position of the other compartment boundary.
3122 .. mdp:: massw-split0
3124 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3128 Use the geometrical center.
3132 Use the center of mass.
3134 .. mdp:: massw-split1
3136 (no) As above, but for split-group #1.
3138 .. mdp:: solvent-group
3140 Name of the index group of solvent molecules.
3142 .. mdp:: coupl-steps
3144 (10) Average the number of ions per compartment over these many swap attempt steps.
3145 This can be used to prevent that ions near a compartment boundary
3146 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3150 (1) The number of different ion types to be controlled. These are during the
3151 simulation exchanged with solvent molecules to reach the desired reference numbers.
3153 .. mdp:: iontype0-name
3155 Name of the first ion type.
3157 .. mdp:: iontype0-in-A
3159 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3160 The default value of -1 means: use the number of ions as found in time step 0
3163 .. mdp:: iontype0-in-B
3165 (-1) Reference number of ions of type 0 for compartment B.
3167 .. mdp:: bulk-offsetA
3169 (0.0) Offset of the first swap layer from the compartment A midplane.
3170 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3171 at maximum distance (= bulk concentration) to the split group layers. However,
3172 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3173 towards one of the compartment-partitioning layers (at +/- 1.0).
3175 .. mdp:: bulk-offsetB
3177 (0.0) Offset of the other swap layer from the compartment B midplane.
3182 (\1) Only swap ions if threshold difference to requested count is reached.
3186 (2.0) [nm] Radius of the split cylinder #0.
3187 Two split cylinders (mimicking the channel pores) can optionally be defined
3188 relative to the center of the split group. With the help of these cylinders
3189 it can be counted which ions have passed which channel. The split cylinder
3190 definition has no impact on whether or not ion/water swaps are done.
3194 (1.0) [nm] Upper extension of the split cylinder #0.
3198 (1.0) [nm] Lower extension of the split cylinder #0.
3202 (2.0) [nm] Radius of the split cylinder #1.
3206 (1.0) [nm] Upper extension of the split cylinder #1.
3210 (1.0) [nm] Lower extension of the split cylinder #1.
3212 Density-guided simulations
3213 ^^^^^^^^^^^^^^^^^^^^^^^^^^
3215 These options enable and control the calculation and application of additional
3216 forces that are derived from three-dimensional densities, e.g., from cryo
3217 electron-microscopy experiments. (See the `reference manual`_ for details)
3219 .. mdp:: density-guided-simulation-active
3221 (no) Activate density-guided simulations.
3223 .. mdp:: density-guided-simulation-group
3225 (protein) The atoms that are subject to the forces from the density-guided
3226 simulation and contribute to the simulated density.
3228 .. mdp:: density-guided-simulation-similarity-measure
3230 (inner-product) Similarity measure between the density that is calculated
3231 from the atom positions and the reference density.
3233 .. mdp-value:: inner-product
3235 Takes the sum of the product of reference density and simulated density
3238 .. mdp-value:: relative-entropy
3240 Uses the negative relative entropy (or Kullback-Leibler divergence)
3241 between reference density and simulated density as similarity measure.
3242 Negative density values are ignored.
3244 .. mdp:: density-guided-simulation-atom-spreading-weight
3246 (unity) Determines the multiplication factor for the Gaussian kernel when
3247 spreading atoms on the grid.
3249 .. mdp-value:: unity
3251 Every atom in the density fitting group is assigned the same unit factor.
3255 Atoms contribute to the simulated density proportional to their mass.
3257 .. mdp-value:: charge
3259 Atoms contribute to the simulated density proportional to their charge.
3261 .. mdp:: density-guided-simulation-force-constant
3263 (1e+09) [kJ mol\ :sup:`-1`] The scaling factor for density-guided simulation
3264 forces. May also be negative.
3266 .. mdp:: density-guided-simulation-gaussian-transform-spreading-width
3268 (0.2) [nm] The Gaussian RMS width for the spread kernel for the simulated
3271 .. mdp:: density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width
3273 (4) The range after which the gaussian is cut off in multiples of the Gaussian
3274 RMS width described above.
3276 .. mdp:: density-guided-simulation-reference-density-filename
3278 (reference.mrc) Reference density file name using an absolute path or a path
3279 relative to the to the folder from which :ref:`gmx mdrun` is called.
3281 .. mdp:: density-guided-simulation-nst
3283 (1) Interval in steps at which the density fitting forces are evaluated
3284 and applied. The forces are scaled by this number when applied (See the
3285 `reference manual`_ for details).
3287 .. mdp:: density-guided-simulation-normalize-densities
3289 (true) Normalize the sum of density voxel values to one for the reference
3290 density as well as the simulated density.
3292 .. mdp:: density-guided-simulation-adaptive-force-scaling
3294 (false) Adapt the force constant to ensure a steady increase in similarity
3295 between simulated and reference density.
3299 Do not use adaptive force scaling.
3303 Use adaptive force scaling.
3305 .. mdp:: density-guided-simulation-adaptive-force-scaling-time-constant
3307 (4) [ps] Couple force constant to increase in similarity with reference density
3308 with this time constant. Larger times result in looser coupling.
3310 User defined thingies
3311 ^^^^^^^^^^^^^^^^^^^^^
3315 .. mdp:: userint1 (0)
3316 .. mdp:: userint2 (0)
3317 .. mdp:: userint3 (0)
3318 .. mdp:: userint4 (0)
3319 .. mdp:: userreal1 (0)
3320 .. mdp:: userreal2 (0)
3321 .. mdp:: userreal3 (0)
3322 .. mdp:: userreal4 (0)
3324 These you can use if you modify code. You can pass integers and
3325 reals and groups to your subroutine. Check the inputrec definition
3326 in ``src/gromacs/mdtypes/inputrec.h``
3331 These features have been removed from |Gromacs|, but so that old
3332 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3333 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3334 fatal error if this is set.
3340 .. mdp:: implicit-solvent
3344 .. _reference manual: gmx-manual-parent-dir_