2 See the "run control" section for a working example of the
3 syntax to use when making .mdp entries, with and without detailed
4 documentation for values those entries might take. Everything can
5 be cross-referenced, see the examples there. TODO Make more
8 Molecular dynamics parameters (.mdp options)
9 ============================================
16 Default values are given in parentheses, or listed first among
17 choices. The first option in the list is always the default
18 option. Units are given in square brackets. The difference between a
19 dash and an underscore is ignored.
21 A :ref:`sample mdp file <mdp>` is available. This should be
22 appropriate to start a normal simulation. Edit it to suit your
23 specific needs and desires.
31 directories to include in your topology. Format:
32 ``-I/home/john/mylib -I../otherlib``
36 defines to pass to the preprocessor, default is no defines. You can
37 use any defines to control options in your customized topology
38 files. Options that act on existing :ref:`top` file mechanisms
41 ``-DFLEXIBLE`` will use flexible water instead of rigid water
42 into your topology, this can be useful for normal mode analysis.
44 ``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
45 your topology, used for implementing position restraints.
53 (Despite the name, this list includes algorithms that are not
54 actually integrators over time. :mdp-value:`integrator=steep` and
55 all entries following it are in this category)
59 A leap-frog algorithm for integrating Newton's equations of motion.
63 A velocity Verlet algorithm for integrating Newton's equations
64 of motion. For constant NVE simulations started from
65 corresponding points in the same trajectory, the trajectories
66 are analytically, but not binary, identical to the
67 :mdp-value:`integrator=md` leap-frog integrator. The kinetic
68 energy, which is determined from the whole step velocities and
69 is therefore slightly too high. The advantage of this integrator
70 is more accurate, reversible Nose-Hoover and Parrinello-Rahman
71 coupling integration based on Trotter expansion, as well as
72 (slightly too small) full step velocity output. This all comes
73 at the cost off extra computation, especially with constraints
74 and extra communication in parallel. Note that for nearly all
75 production simulations the :mdp-value:`integrator=md` integrator
78 .. mdp-value:: md-vv-avek
80 A velocity Verlet algorithm identical to
81 :mdp-value:`integrator=md-vv`, except that the kinetic energy is
82 determined as the average of the two half step kinetic energies
83 as in the :mdp-value:`integrator=md` integrator, and this thus
84 more accurate. With Nose-Hoover and/or Parrinello-Rahman
85 coupling this comes with a slight increase in computational
90 An accurate and efficient leap-frog stochastic dynamics
91 integrator. With constraints, coordinates needs to be
92 constrained twice per integration step. Depending on the
93 computational cost of the force calculation, this can take a
94 significant part of the simulation time. The temperature for one
95 or more groups of atoms (:mdp:`tc-grps`) is set with
96 :mdp:`ref-t`, the inverse friction constant for each group is
97 set with :mdp:`tau-t`. The parameters :mdp:`tcoupl` and :mdp:`nsttcouple`
98 are ignored. The random generator is initialized with
99 :mdp:`ld-seed`. When used as a thermostat, an appropriate value
100 for :mdp:`tau-t` is 2 ps, since this results in a friction that
101 is lower than the internal friction of water, while it is high
102 enough to remove excess heat NOTE: temperature deviations decay
103 twice as fast as with a Berendsen thermostat with the same
108 An Euler integrator for Brownian or position Langevin dynamics,
109 the velocity is the force divided by a friction coefficient
110 (:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
111 :mdp:`bd-fric` is 0, the friction coefficient for each particle
112 is calculated as mass/ :mdp:`tau-t`, as for the integrator
113 :mdp-value:`integrator=sd`. The random generator is initialized
118 A steepest descent algorithm for energy minimization. The
119 maximum step size is :mdp:`emstep`, the tolerance is
124 A conjugate gradient algorithm for energy minimization, the
125 tolerance is :mdp:`emtol`. CG is more efficient when a steepest
126 descent step is done every once in a while, this is determined
127 by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
128 analysis, which requires a very high accuracy, |Gromacs| should be
129 compiled in double precision.
131 .. mdp-value:: l-bfgs
133 A quasi-Newtonian algorithm for energy minimization according to
134 the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
135 practice this seems to converge faster than Conjugate Gradients,
136 but due to the correction steps necessary it is not (yet)
141 Normal mode analysis is performed on the structure in the :ref:`tpr`
142 file. |Gromacs| should be compiled in double precision.
146 Test particle insertion. The last molecule in the topology is
147 the test particle. A trajectory must be provided to ``mdrun
148 -rerun``. This trajectory should not contain the molecule to be
149 inserted. Insertions are performed :mdp:`nsteps` times in each
150 frame at random locations and with random orientiations of the
151 molecule. When :mdp:`nstlist` is larger than one,
152 :mdp:`nstlist` insertions are performed in a sphere with radius
153 :mdp:`rtpi` around a the same random location using the same
154 pair list. Since pair list construction is expensive,
155 one can perform several extra insertions with the same list
156 almost for free. The random seed is set with
157 :mdp:`ld-seed`. The temperature for the Boltzmann weighting is
158 set with :mdp:`ref-t`, this should match the temperature of the
159 simulation of the original trajectory. Dispersion correction is
160 implemented correctly for TPI. All relevant quantities are
161 written to the file specified with ``mdrun -tpi``. The
162 distribution of insertion energies is written to the file
163 specified with ``mdrun -tpid``. No trajectory or energy file is
164 written. Parallel TPI gives identical results to single-node
165 TPI. For charged molecules, using PME with a fine grid is most
166 accurate and also efficient, since the potential in the system
167 only needs to be calculated once per frame.
171 Test particle insertion into a predefined cavity location. The
172 procedure is the same as for :mdp-value:`integrator=tpi`, except
173 that one coordinate extra is read from the trajectory, which is
174 used as the insertion location. The molecule to be inserted
175 should be centered at 0,0,0. |Gromacs| does not do this for you,
176 since for different situations a different way of centering
177 might be optimal. Also :mdp:`rtpi` sets the radius for the
178 sphere around this location. Neighbor searching is done only
179 once per frame, :mdp:`nstlist` is not used. Parallel
180 :mdp-value:`integrator=tpic` gives identical results to
181 single-rank :mdp-value:`integrator=tpic`.
185 Enable MiMiC QM/MM coupling to run hybrid molecular dynamics.
186 Keey in mind that its required to launch CPMD compiled with MiMiC as well.
187 In this mode all options regarding integration (T-coupling, P-coupling,
188 timestep and number of steps) are ignored as CPMD will do the integration
189 instead. Options related to forces computation (cutoffs, PME parameters,
190 etc.) are working as usual. Atom selection to define QM atoms is read
191 from :mdp:`QMMM-grps`
196 starting time for your run (only makes sense for time-based
202 time step for integration (only makes sense for time-based
208 maximum number of steps to integrate or minimize, -1 is no
214 The starting step. The time at step i in a run is
215 calculated as: t = :mdp:`tinit` + :mdp:`dt` *
216 (:mdp:`init-step` + i). The free-energy lambda is calculated
217 as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
218 (:mdp:`init-step` + i). Also non-equilibrium MD parameters can
219 depend on the step number. Thus for exact restarts or redoing
220 part of a run it might be necessary to set :mdp:`init-step` to
221 the step number of the restart frame. :ref:`gmx convert-tpr`
222 does this automatically.
224 .. mdp:: simulation-part
227 A simulation can consist of multiple parts, each of which has
228 a part number. This option specifies what that number will
229 be, which helps keep track of parts that are logically the
230 same simulation. This option is generally useful to set only
231 when coping with a crashed simulation where files were lost.
235 .. mdp-value:: Linear
237 Remove center of mass translational velocity
239 .. mdp-value:: Angular
241 Remove center of mass translational and rotational velocity
243 .. mdp-value:: Linear-acceleration-correction
245 Remove center of mass translational velocity. Correct the center of
246 mass position assuming linear acceleration over :mdp:`nstcomm` steps.
247 This is useful for cases where an acceleration is expected on the
248 center of mass which is nearly constant over :mdp:`nstcomm` steps.
249 This can occur for example when pulling on a group using an absolute
254 No restriction on the center of mass motion
259 frequency for center of mass motion removal
263 group(s) for center of mass motion removal, default is the whole
272 (0) [amu ps\ :sup:`-1`]
273 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
274 the friction coefficient for each particle is calculated as mass/
280 used to initialize random generator for thermal noise for
281 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
282 a pseudo random seed is used. When running BD or SD on multiple
283 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
284 the processor number.
292 (10.0) [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
293 the minimization is converged when the maximum force is smaller
304 frequency of performing 1 steepest descent step while doing
305 conjugate gradient energy minimization.
310 Number of correction steps to use for L-BFGS minimization. A higher
311 number is (at least theoretically) more accurate, but slower.
314 Shell Molecular Dynamics
315 ^^^^^^^^^^^^^^^^^^^^^^^^
317 When shells or flexible constraints are present in the system the
318 positions of the shells and the lengths of the flexible constraints
319 are optimized at every time step until either the RMS force on the
320 shells and constraints is less than :mdp:`emtol`, or a maximum number
321 of iterations :mdp:`niter` has been reached. Minimization is converged
322 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
323 value should be 1.0 at most.
328 maximum number of iterations for optimizing the shell positions and
329 the flexible constraints.
334 the step size for optimizing the flexible constraints. Should be
335 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
336 particles in a flexible constraint and d2V/dq2 is the second
337 derivative of the potential in the constraint direction. Hopefully
338 this number does not differ too much between the flexible
339 constraints, as the number of iterations and thus the runtime is
340 very sensitive to fcstep. Try several values!
343 Test particle insertion
344 ^^^^^^^^^^^^^^^^^^^^^^^
349 the test particle insertion radius, see integrators
350 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
359 number of steps that elapse between writing coordinates to the output
360 trajectory file (:ref:`trr`), the last coordinates are always written
361 unless 0, which means coordinates are not written into the trajectory
367 number of steps that elapse between writing velocities to the output
368 trajectory file (:ref:`trr`), the last velocities are always written
369 unless 0, which means velocities are not written into the trajectory
375 number of steps that elapse between writing forces to the output
376 trajectory file (:ref:`trr`), the last forces are always written,
377 unless 0, which means forces are not written into the trajectory
383 number of steps that elapse between writing energies to the log
384 file, the last energies are always written.
386 .. mdp:: nstcalcenergy
389 number of steps that elapse between calculating the energies, 0 is
390 never. This option is only relevant with dynamics. This option affects the
391 performance in parallel simulations, because calculating energies
392 requires global communication between all processes which can
393 become a bottleneck at high parallelization.
398 number of steps that elapse between writing energies to energy file,
399 the last energies are always written, should be a multiple of
400 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
401 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
402 energy file, so :ref:`gmx energy` can report exact energy averages
403 and fluctuations also when :mdp:`nstenergy` > 1
405 .. mdp:: nstxout-compressed
408 number of steps that elapse between writing position coordinates
409 using lossy compression (:ref:`xtc` file), 0 for not writing
410 compressed coordinates output.
412 .. mdp:: compressed-x-precision
415 precision with which to write to the compressed trajectory file
417 .. mdp:: compressed-x-grps
419 group(s) to write to the compressed trajectory file, by default the
420 whole system is written (if :mdp:`nstxout-compressed` > 0)
424 group(s) for which to write to write short-ranged non-bonded
425 potential energies to the energy file (not supported on GPUs)
431 .. mdp:: cutoff-scheme
433 .. mdp-value:: Verlet
435 Generate a pair list with buffering. The buffer size is
436 automatically set based on :mdp:`verlet-buffer-tolerance`,
437 unless this is set to -1, in which case :mdp:`rlist` will be
442 Generate a pair list for groups of atoms, corresponding
443 to the charge groups in the topology. This option is no longer
452 Frequency to update the neighbor list. When dynamics and
453 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
454 a minimum value and :ref:`gmx mdrun` might increase it, unless
455 it is set to 1. With parallel simulations and/or non-bonded
456 force calculation on the GPU, a value of 20 or 40 often gives
457 the best performance.
461 The neighbor list is only constructed once and never
462 updated. This is mainly useful for vacuum simulations in which
463 all particles see each other. But vacuum simulations are
464 (temporarily) not supported.
474 Use periodic boundary conditions in all directions.
478 Use no periodic boundary conditions, ignore the box. To simulate
479 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
480 best performance without cut-offs on a single MPI rank, set
481 :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`.
485 Use periodic boundary conditions in x and y directions
486 only. This works only with :mdp-value:`ns-type=grid` and can be used
487 in combination with walls_. Without walls or with only one wall
488 the system size is infinite in the z direction. Therefore
489 pressure coupling or Ewald summation methods can not be
490 used. These disadvantages do not apply when two walls are used.
492 .. mdp:: periodic-molecules
496 molecules are finite, fast molecular PBC can be used
500 for systems with molecules that couple to themselves through the
501 periodic boundary conditions, this requires a slower PBC
502 algorithm and molecules are not made whole in the output
504 .. mdp:: verlet-buffer-tolerance
506 (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
508 Used when performing a simulation with dynamics. This sets
509 the maximum allowed error for pair interactions per particle caused
510 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
511 :mdp:`nstlist` and the Verlet buffer size are fixed (for
512 performance reasons), particle pairs not in the pair list can
513 occasionally get within the cut-off distance during
514 :mdp:`nstlist` -1 steps. This causes very small jumps in the
515 energy. In a constant-temperature ensemble, these very small energy
516 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
517 estimate assumes a homogeneous particle distribution, hence the
518 errors might be slightly underestimated for multi-phase
519 systems. (See the `reference manual`_ for details). For longer
520 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
521 overestimated, because the interactions between particles are
522 ignored. Combined with cancellation of errors, the actual drift of
523 the total energy is usually one to two orders of magnitude
524 smaller. Note that the generated buffer size takes into account
525 that the |Gromacs| pair-list setup leads to a reduction in the
526 drift by a factor 10, compared to a simple particle-pair based
527 list. Without dynamics (energy minimization etc.), the buffer is 5%
528 of the cut-off. For NVE simulations the initial temperature is
529 used, unless this is zero, in which case a buffer of 10% is
530 used. For NVE simulations the tolerance usually needs to be lowered
531 to achieve proper energy conservation on the nanosecond time
532 scale. To override the automated buffer setting, use
533 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
538 Cut-off distance for the short-range neighbor list. With dynamics,
539 this is by default set by the :mdp:`verlet-buffer-tolerance` option
540 and the value of :mdp:`rlist` is ignored. Without dynamics, this
541 is by default set to the maximum cut-off plus 5% buffer, except
542 for test particle insertion, where the buffer is managed exactly
543 and automatically. For NVE simulations, where the automated
544 setting is not possible, the advised procedure is to run :ref:`gmx grompp`
545 with an NVT setup with the expected temperature and copy the resulting
546 value of :mdp:`rlist` to the NVE setup.
554 .. mdp-value:: Cut-off
556 Plain cut-off with pair list radius :mdp:`rlist` and
557 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
562 Classical Ewald sum electrostatics. The real-space cut-off
563 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
564 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
565 of wave vectors used in reciprocal space is controlled by
566 :mdp:`fourierspacing`. The relative accuracy of
567 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
569 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
570 large systems. It is included mainly for reference - in most
571 cases PME will perform much better.
575 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
576 space is similar to the Ewald sum, while the reciprocal part is
577 performed with FFTs. Grid dimensions are controlled with
578 :mdp:`fourierspacing` and the interpolation order with
579 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
580 interpolation the electrostatic forces have an accuracy of
581 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
582 this you might try 0.15 nm. When running in parallel the
583 interpolation parallelizes better than the FFT, so try
584 decreasing grid dimensions while increasing interpolation.
586 .. mdp-value:: P3M-AD
588 Particle-Particle Particle-Mesh algorithm with analytical
589 derivative for for long range electrostatic interactions. The
590 method and code is identical to SPME, except that the influence
591 function is optimized for the grid. This gives a slight increase
594 .. mdp-value:: Reaction-Field
596 Reaction field electrostatics with Coulomb cut-off
597 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
598 dielectric constant beyond the cut-off is
599 :mdp:`epsilon-rf`. The dielectric constant can be set to
600 infinity by setting :mdp:`epsilon-rf` =0.
604 Currently unsupported.
605 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
606 with user-defined potential functions for repulsion, dispersion
607 and Coulomb. When pair interactions are present, :ref:`gmx
608 mdrun` also expects to find a file ``tablep.xvg`` for the pair
609 interactions. When the same interactions should be used for
610 non-bonded and pair interactions the user can specify the same
611 file name for both table files. These files should contain 7
612 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
613 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
614 function, ``g(x)`` the dispersion function and ``h(x)`` the
615 repulsion function. When :mdp:`vdwtype` is not set to User the
616 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
617 the non-bonded interactions ``x`` values should run from 0 to
618 the largest cut-off distance + :mdp:`table-extension` and
619 should be uniformly spaced. For the pair interactions the table
620 length in the file will be used. The optimal spacing, which is
621 used for non-user tables, is ``0.002 nm`` when you run in mixed
622 precision or ``0.0005 nm`` when you run in double precision. The
623 function value at ``x=0`` is not important. More information is
624 in the printed manual.
626 .. mdp-value:: PME-Switch
628 Currently unsupported.
629 A combination of PME and a switch function for the direct-space
630 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
633 .. mdp-value:: PME-User
635 Currently unsupported.
636 A combination of PME and user tables (see
637 above). :mdp:`rcoulomb` is allowed to be smaller than
638 :mdp:`rlist`. The PME mesh contribution is subtracted from the
639 user table by :ref:`gmx mdrun`. Because of this subtraction the
640 user tables should contain about 10 decimal places.
642 .. mdp-value:: PME-User-Switch
644 Currently unsupported.
645 A combination of PME-User and a switching function (see
646 above). The switching function is applied to final
647 particle-particle interaction, *i.e.* both to the user supplied
648 function and the PME Mesh correction part.
650 .. mdp:: coulomb-modifier
652 .. mdp-value:: Potential-shift
654 Shift the Coulomb potential by a constant such that it is zero
655 at the cut-off. This makes the potential the integral of the
656 force. Note that this does not affect the forces or the
661 Use an unmodified Coulomb potential. This can be useful
662 when comparing energies with those computed with other software.
664 .. mdp:: rcoulomb-switch
667 where to start switching the Coulomb potential, only relevant
668 when force or potential switching is used
673 The distance for the Coulomb cut-off. Note that with PME this value
674 can be increased by the PME tuning in :ref:`gmx mdrun` along with
675 the PME grid spacing.
680 The relative dielectric constant. A value of 0 means infinity.
685 The relative dielectric constant of the reaction field. This
686 is only used with reaction-field electrostatics. A value of 0
695 .. mdp-value:: Cut-off
697 Plain cut-off with pair list radius :mdp:`rlist` and VdW
698 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
702 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
703 grid dimensions are controlled with :mdp:`fourierspacing` in
704 the same way as for electrostatics, and the interpolation order
705 is controlled with :mdp:`pme-order`. The relative accuracy of
706 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
707 and the specific combination rules that are to be used by the
708 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
712 This functionality is deprecated and replaced by using
713 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
714 The LJ (not Buckingham) potential is decreased over the whole range and
715 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
718 .. mdp-value:: Switch
720 This functionality is deprecated and replaced by using
721 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
722 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
723 which it is switched off to reach zero at :mdp:`rvdw`. Both the
724 potential and force functions are continuously smooth, but be
725 aware that all switch functions will give rise to a bulge
726 (increase) in the force (since we are switching the
731 Currently unsupported.
732 See user for :mdp:`coulombtype`. The function value at zero is
733 not important. When you want to use LJ correction, make sure
734 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
735 function. When :mdp:`coulombtype` is not set to User the values
736 for the ``f`` and ``-f'`` columns are ignored.
738 .. mdp:: vdw-modifier
740 .. mdp-value:: Potential-shift
742 Shift the Van der Waals potential by a constant such that it is
743 zero at the cut-off. This makes the potential the integral of
744 the force. Note that this does not affect the forces or the
749 Use an unmodified Van der Waals potential. This can be useful
750 when comparing energies with those computed with other software.
752 .. mdp-value:: Force-switch
754 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
755 and :mdp:`rvdw`. This shifts the potential shift over the whole
756 range and switches it to zero at the cut-off. Note that this is
757 more expensive to calculate than a plain cut-off and it is not
758 required for energy conservation, since Potential-shift
759 conserves energy just as well.
761 .. mdp-value:: Potential-switch
763 Smoothly switches the potential to zero between
764 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
765 articifically large forces in the switching region and is much
766 more expensive to calculate. This option should only be used if
767 the force field you are using requires this.
772 where to start switching the LJ force and possibly the potential,
773 only relevant when force or potential switching is used
778 distance for the LJ or Buckingham cut-off
784 don't apply any correction
786 .. mdp-value:: EnerPres
788 apply long range dispersion corrections for Energy and Pressure
792 apply long range dispersion corrections for Energy only
798 .. mdp:: table-extension
801 Extension of the non-bonded potential lookup tables beyond the
802 largest cut-off distance. With actual non-bonded interactions
803 the tables are never accessed beyond the cut-off. But a longer
804 table length might be needed for the 1-4 interactions, which
805 are always tabulated irrespective of the use of tables for
806 the non-bonded interactions.
808 .. mdp:: energygrp-table
810 Currently unsupported.
811 When user tables are used for electrostatics and/or VdW, here one
812 can give pairs of energy groups for which seperate user tables
813 should be used. The two energy groups will be appended to the table
814 file name, in order of their definition in :mdp:`energygrps`,
815 seperated by underscores. For example, if ``energygrps = Na Cl
816 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
817 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
818 normal ``table.xvg`` which will be used for all other energy group
825 .. mdp:: fourierspacing
828 For ordinary Ewald, the ratio of the box dimensions and the spacing
829 determines a lower bound for the number of wave vectors to use in
830 each (signed) direction. For PME and P3M, that ratio determines a
831 lower bound for the number of Fourier-space grid points that will
832 be used along that axis. In all cases, the number for each
833 direction can be overridden by entering a non-zero value for that
834 :mdp:`fourier-nx` direction. For optimizing the relative load of
835 the particle-particle interactions and the mesh part of PME, it is
836 useful to know that the accuracy of the electrostatics remains
837 nearly constant when the Coulomb cut-off and the PME grid spacing
838 are scaled by the same factor. Note that this spacing can be scaled
839 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
846 Highest magnitude of wave vectors in reciprocal space when using Ewald.
847 Grid size when using PME or P3M. These values override
848 :mdp:`fourierspacing` per direction. The best choice is powers of
849 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
850 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
856 Interpolation order for PME. 4 equals cubic interpolation. You
857 might try 6/8/10 when running in parallel and simultaneously
858 decrease grid dimension.
863 The relative strength of the Ewald-shifted direct potential at
864 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
865 will give a more accurate direct sum, but then you need more wave
866 vectors for the reciprocal sum.
868 .. mdp:: ewald-rtol-lj
871 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
872 to control the relative strength of the dispersion potential at
873 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
874 electrostatic potential.
876 .. mdp:: lj-pme-comb-rule
879 The combination rules used to combine VdW-parameters in the
880 reciprocal part of LJ-PME. Geometric rules are much faster than
881 Lorentz-Berthelot and usually the recommended choice, even when the
882 rest of the force field uses the Lorentz-Berthelot rules.
884 .. mdp-value:: Geometric
886 Apply geometric combination rules
888 .. mdp-value:: Lorentz-Berthelot
890 Apply Lorentz-Berthelot combination rules
892 .. mdp:: ewald-geometry
896 The Ewald sum is performed in all three dimensions.
900 The reciprocal sum is still performed in 3D, but a force and
901 potential correction applied in the ``z`` dimension to produce a
902 pseudo-2D summation. If your system has a slab geometry in the
903 ``x-y`` plane you can try to increase the ``z``-dimension of the box
904 (a box height of 3 times the slab height is usually ok) and use
907 .. mdp:: epsilon-surface
910 This controls the dipole correction to the Ewald summation in
911 3D. The default value of zero means it is turned off. Turn it on by
912 setting it to the value of the relative permittivity of the
913 imaginary surface around your infinite system. Be careful - you
914 shouldn't use this if you have free mobile charges in your
915 system. This value does not affect the slab 3DC variant of the long
926 No temperature coupling.
928 .. mdp-value:: berendsen
930 Temperature coupling with a Berendsen thermostat to a bath with
931 temperature :mdp:`ref-t`, with time constant
932 :mdp:`tau-t`. Several groups can be coupled separately, these
933 are specified in the :mdp:`tc-grps` field separated by spaces.
935 .. mdp-value:: nose-hoover
937 Temperature coupling using a Nose-Hoover extended ensemble. The
938 reference temperature and coupling groups are selected as above,
939 but in this case :mdp:`tau-t` controls the period of the
940 temperature fluctuations at equilibrium, which is slightly
941 different from a relaxation time. For NVT simulations the
942 conserved energy quantity is written to the energy and log files.
944 .. mdp-value:: andersen
946 Temperature coupling by randomizing a fraction of the particle velocities
947 at each timestep. Reference temperature and coupling groups are
948 selected as above. :mdp:`tau-t` is the average time between
949 randomization of each molecule. Inhibits particle dynamics
950 somewhat, but little or no ergodicity issues. Currently only
951 implemented with velocity Verlet, and not implemented with
954 .. mdp-value:: andersen-massive
956 Temperature coupling by randomizing velocities of all particles at
957 infrequent timesteps. Reference temperature and coupling groups are
958 selected as above. :mdp:`tau-t` is the time between
959 randomization of all molecules. Inhibits particle dynamics
960 somewhat, but little or no ergodicity issues. Currently only
961 implemented with velocity Verlet.
963 .. mdp-value:: v-rescale
965 Temperature coupling using velocity rescaling with a stochastic
966 term (JCP 126, 014101). This thermostat is similar to Berendsen
967 coupling, with the same scaling using :mdp:`tau-t`, but the
968 stochastic term ensures that a proper canonical ensemble is
969 generated. The random seed is set with :mdp:`ld-seed`. This
970 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
971 simulations the conserved energy quantity is written to the
977 The frequency for coupling the temperature. The default value of -1
978 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
979 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
980 Verlet integrators :mdp:`nsttcouple` is set to 1.
982 .. mdp:: nh-chain-length
985 The number of chained Nose-Hoover thermostats for velocity Verlet
986 integrators, the leap-frog :mdp-value:`integrator=md` integrator
987 only supports 1. Data for the NH chain variables is not printed
988 to the :ref:`edr` file by default, but can be turned on with the
989 :mdp:`print-nose-hoover-chain-variables` option.
991 .. mdp:: print-nose-hoover-chain-variables
995 Do not store Nose-Hoover chain variables in the energy file.
999 Store all positions and velocities of the Nose-Hoover chain
1004 groups to couple to separate temperature baths
1009 time constant for coupling (one for each group in
1010 :mdp:`tc-grps`), -1 means no temperature coupling
1015 reference temperature for coupling (one for each group in
1026 No pressure coupling. This means a fixed box size.
1028 .. mdp-value:: Berendsen
1030 Exponential relaxation pressure coupling with time constant
1031 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1032 argued that this does not yield a correct thermodynamic
1033 ensemble, but it is the most efficient way to scale a box at the
1036 .. mdp-value:: Parrinello-Rahman
1038 Extended-ensemble pressure coupling where the box vectors are
1039 subject to an equation of motion. The equation of motion for the
1040 atoms is coupled to this. No instantaneous scaling takes
1041 place. As for Nose-Hoover temperature coupling the time constant
1042 :mdp:`tau-p` is the period of pressure fluctuations at
1043 equilibrium. This is probably a better method when you want to
1044 apply pressure scaling during data collection, but beware that
1045 you can get very large oscillations if you are starting from a
1046 different pressure. For simulations where the exact fluctations
1047 of the NPT ensemble are important, or if the pressure coupling
1048 time is very short it may not be appropriate, as the previous
1049 time step pressure is used in some steps of the |Gromacs|
1050 implementation for the current time step pressure.
1054 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1055 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1056 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1057 time constant :mdp:`tau-p` is the period of pressure
1058 fluctuations at equilibrium. This is probably a better method
1059 when you want to apply pressure scaling during data collection,
1060 but beware that you can get very large oscillations if you are
1061 starting from a different pressure. Currently (as of version
1062 5.1), it only supports isotropic scaling, and only works without
1067 Specifies the kind of isotropy of the pressure coupling used. Each
1068 kind takes one or more values for :mdp:`compressibility` and
1069 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1071 .. mdp-value:: isotropic
1073 Isotropic pressure coupling with time constant
1074 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1075 :mdp:`ref-p` is required.
1077 .. mdp-value:: semiisotropic
1079 Pressure coupling which is isotropic in the ``x`` and ``y``
1080 direction, but different in the ``z`` direction. This can be
1081 useful for membrane simulations. Two values each for
1082 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1083 ``x/y`` and ``z`` directions respectively.
1085 .. mdp-value:: anisotropic
1087 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1088 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1089 respectively. When the off-diagonal compressibilities are set to
1090 zero, a rectangular box will stay rectangular. Beware that
1091 anisotropic scaling can lead to extreme deformation of the
1094 .. mdp-value:: surface-tension
1096 Surface tension coupling for surfaces parallel to the
1097 xy-plane. Uses normal pressure coupling for the ``z``-direction,
1098 while the surface tension is coupled to the ``x/y`` dimensions of
1099 the box. The first :mdp:`ref-p` value is the reference surface
1100 tension times the number of surfaces ``bar nm``, the second
1101 value is the reference ``z``-pressure ``bar``. The two
1102 :mdp:`compressibility` values are the compressibility in the
1103 ``x/y`` and ``z`` direction respectively. The value for the
1104 ``z``-compressibility should be reasonably accurate since it
1105 influences the convergence of the surface-tension, it can also
1106 be set to zero to have a box with constant height.
1111 The frequency for coupling the pressure. The default value of -1
1112 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1113 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1114 Verlet integrators :mdp:`nstpcouple` is set to 1.
1119 The time constant for pressure coupling (one value for all
1122 .. mdp:: compressibility
1125 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1126 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1127 required values is implied by :mdp:`pcoupltype`.
1132 The reference pressure for coupling. The number of required values
1133 is implied by :mdp:`pcoupltype`.
1135 .. mdp:: refcoord-scaling
1139 The reference coordinates for position restraints are not
1140 modified. Note that with this option the virial and pressure
1141 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1146 The reference coordinates are scaled with the scaling matrix of
1147 the pressure coupling.
1151 Scale the center of mass of the reference coordinates with the
1152 scaling matrix of the pressure coupling. The vectors of each
1153 reference coordinate to the center of mass are not scaled. Only
1154 one COM is used, even when there are multiple molecules with
1155 position restraints. For calculating the COM of the reference
1156 coordinates in the starting configuration, periodic boundary
1157 conditions are not taken into account. Note that with this option
1158 the virial and pressure might be ill defined, see
1159 :ref:`here <reference-manual-position-restraints>` for more details.
1165 Simulated annealing is controlled separately for each temperature
1166 group in |Gromacs|. The reference temperature is a piecewise linear
1167 function, but you can use an arbitrary number of points for each
1168 group, and choose either a single sequence or a periodic behaviour for
1169 each group. The actual annealing is performed by dynamically changing
1170 the reference temperature used in the thermostat algorithm selected,
1171 so remember that the system will usually not instantaneously reach the
1172 reference temperature!
1176 Type of annealing for each temperature group
1180 No simulated annealing - just couple to reference temperature value.
1182 .. mdp-value:: single
1184 A single sequence of annealing points. If your simulation is
1185 longer than the time of the last point, the temperature will be
1186 coupled to this constant value after the annealing sequence has
1187 reached the last time point.
1189 .. mdp-value:: periodic
1191 The annealing will start over at the first reference point once
1192 the last reference time is reached. This is repeated until the
1195 .. mdp:: annealing-npoints
1197 A list with the number of annealing reference/control points used
1198 for each temperature group. Use 0 for groups that are not
1199 annealed. The number of entries should equal the number of
1202 .. mdp:: annealing-time
1204 List of times at the annealing reference/control points for each
1205 group. If you are using periodic annealing, the times will be used
1206 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1207 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1208 etc. The number of entries should equal the sum of the numbers
1209 given in :mdp:`annealing-npoints`.
1211 .. mdp:: annealing-temp
1213 List of temperatures at the annealing reference/control points for
1214 each group. The number of entries should equal the sum of the
1215 numbers given in :mdp:`annealing-npoints`.
1217 Confused? OK, let's use an example. Assume you have two temperature
1218 groups, set the group selections to ``annealing = single periodic``,
1219 the number of points of each group to ``annealing-npoints = 3 4``, the
1220 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1221 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1222 will be coupled to 298K at 0ps, but the reference temperature will
1223 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1224 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1225 second group is coupled to 298K at 0ps, it increases linearly to 320K
1226 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1227 decreases to 298K, and then it starts over with the same pattern
1228 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1229 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1239 Do not generate velocities. The velocities are set to zero
1240 when there are no velocities in the input structure file.
1244 Generate velocities in :ref:`gmx grompp` according to a
1245 Maxwell distribution at temperature :mdp:`gen-temp`, with
1246 random seed :mdp:`gen-seed`. This is only meaningful with
1247 :mdp-value:`integrator=md`.
1252 temperature for Maxwell distribution
1257 used to initialize random generator for random velocities,
1258 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1265 .. mdp:: constraints
1267 Controls which bonds in the topology will be converted to rigid
1268 holonomic constraints. Note that typical rigid water models do not
1269 have bonds, but rather a specialized ``[settles]`` directive, so
1270 are not affected by this keyword.
1274 No bonds converted to constraints.
1276 .. mdp-value:: h-bonds
1278 Convert the bonds with H-atoms to constraints.
1280 .. mdp-value:: all-bonds
1282 Convert all bonds to constraints.
1284 .. mdp-value:: h-angles
1286 Convert all bonds to constraints and convert the angles that
1287 involve H-atoms to bond-constraints.
1289 .. mdp-value:: all-angles
1291 Convert all bonds to constraints and all angles to bond-constraints.
1293 .. mdp:: constraint-algorithm
1295 Chooses which solver satisfies any non-SETTLE holonomic
1298 .. mdp-value:: LINCS
1300 LINear Constraint Solver. With domain decomposition the parallel
1301 version P-LINCS is used. The accuracy in set with
1302 :mdp:`lincs-order`, which sets the number of matrices in the
1303 expansion for the matrix inversion. After the matrix inversion
1304 correction the algorithm does an iterative correction to
1305 compensate for lengthening due to rotation. The number of such
1306 iterations can be controlled with :mdp:`lincs-iter`. The root
1307 mean square relative constraint deviation is printed to the log
1308 file every :mdp:`nstlog` steps. If a bond rotates more than
1309 :mdp:`lincs-warnangle` in one step, a warning will be printed
1310 both to the log file and to ``stderr``. LINCS should not be used
1311 with coupled angle constraints.
1313 .. mdp-value:: SHAKE
1315 SHAKE is slightly slower and less stable than LINCS, but does
1316 work with angle constraints. The relative tolerance is set with
1317 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1318 does not support constraints between atoms on different
1319 decomposition domains, so it can only be used with domain
1320 decomposition when so-called update-groups are used, which is
1321 usally the case when only bonds involving hydrogens are
1322 constrained. SHAKE can not be used with energy minimization.
1324 .. mdp:: continuation
1326 This option was formerly known as ``unconstrained-start``.
1330 apply constraints to the start configuration and reset shells
1334 do not apply constraints to the start configuration and do not
1335 reset shells, useful for exact coninuation and reruns
1340 relative tolerance for SHAKE
1342 .. mdp:: lincs-order
1345 Highest order in the expansion of the constraint coupling
1346 matrix. When constraints form triangles, an additional expansion of
1347 the same order is applied on top of the normal expansion only for
1348 the couplings within such triangles. For "normal" MD simulations an
1349 order of 4 usually suffices, 6 is needed for large time-steps with
1350 virtual sites or BD. For accurate energy minimization an order of 8
1351 or more might be required. With domain decomposition, the cell size
1352 is limited by the distance spanned by :mdp:`lincs-order` +1
1353 constraints. When one wants to scale further than this limit, one
1354 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1355 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1356 )* :mdp:`lincs-order` remains constant.
1361 Number of iterations to correct for rotational lengthening in
1362 LINCS. For normal runs a single step is sufficient, but for NVE
1363 runs where you want to conserve energy accurately or for accurate
1364 energy minimization you might want to increase it to 2.
1366 .. mdp:: lincs-warnangle
1369 maximum angle that a bond can rotate before LINCS will complain
1375 bonds are represented by a harmonic potential
1379 bonds are represented by a Morse potential
1382 Energy group exclusions
1383 ^^^^^^^^^^^^^^^^^^^^^^^
1385 .. mdp:: energygrp-excl
1387 Pairs of energy groups for which all non-bonded interactions are
1388 excluded. An example: if you have two energy groups ``Protein`` and
1389 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1390 would give only the non-bonded interactions between the protein and
1391 the solvent. This is especially useful for speeding up energy
1392 calculations with ``mdrun -rerun`` and for excluding interactions
1393 within frozen groups.
1402 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1403 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1404 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1405 used (it is usually best to use semiisotropic pressure coupling
1406 with the ``x/y`` compressibility set to 0, as otherwise the surface
1407 area will change). Walls interact wit the rest of the system
1408 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1409 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1410 monitor the interaction of energy groups with each wall. The center
1411 of mass motion removal will be turned off in the ``z``-direction.
1413 .. mdp:: wall-atomtype
1415 the atom type name in the force field for each wall. By (for
1416 example) defining a special wall atom type in the topology with its
1417 own combination rules, this allows for independent tuning of the
1418 interaction of each atomtype with the walls.
1424 LJ integrated over the volume behind the wall: 9-3 potential
1428 LJ integrated over the wall surface: 10-4 potential
1432 direct LJ potential with the ``z`` distance from the wall
1436 user defined potentials indexed with the ``z`` distance from the
1437 wall, the tables are read analogously to the
1438 :mdp:`energygrp-table` option, where the first name is for a
1439 "normal" energy group and the second name is ``wall0`` or
1440 ``wall1``, only the dispersion and repulsion columns are used
1442 .. mdp:: wall-r-linpot
1445 Below this distance from the wall the potential is continued
1446 linearly and thus the force is constant. Setting this option to a
1447 postive value is especially useful for equilibration when some
1448 atoms are beyond a wall. When the value is <=0 (<0 for
1449 :mdp:`wall-type` =table), a fatal error is generated when atoms
1452 .. mdp:: wall-density
1454 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1455 the number density of the atoms for each wall for wall types 9-3
1458 .. mdp:: wall-ewald-zfac
1461 The scaling factor for the third box vector for Ewald summation
1462 only, the minimum is 2. Ewald summation can only be used with
1463 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1464 ``=3dc``. The empty layer in the box serves to decrease the
1465 unphysical Coulomb interaction between periodic images.
1471 Note that where pulling coordinates are applicable, there can be more
1472 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1473 variables will exist accordingly. Documentation references to things
1474 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1475 applicable pulling coordinate, eg. the second pull coordinate is described by
1476 pull-coord2-vec, pull-coord2-k, and so on.
1482 No center of mass pulling. All the following pull options will
1483 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1488 Center of mass pulling will be applied on 1 or more groups using
1489 1 or more pull coordinates.
1491 .. mdp:: pull-cylinder-r
1494 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1496 .. mdp:: pull-constr-tol
1499 the relative constraint tolerance for constraint pulling
1501 .. mdp:: pull-print-com
1505 do not print the COM for any group
1509 print the COM of all groups for all pull coordinates
1511 .. mdp:: pull-print-ref-value
1515 do not print the reference value for each pull coordinate
1519 print the reference value for each pull coordinate
1521 .. mdp:: pull-print-components
1525 only print the distance for each pull coordinate
1529 print the distance and Cartesian components selected in
1530 :mdp:`pull-coord1-dim`
1532 .. mdp:: pull-nstxout
1535 frequency for writing out the COMs of all the pull group (0 is
1538 .. mdp:: pull-nstfout
1541 frequency for writing out the force of all the pulled group
1544 .. mdp:: pull-pbc-ref-prev-step-com
1548 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1549 treatment of periodic boundary conditions.
1553 Use the COM of the previous step as reference for the treatment
1554 of periodic boundary conditions. The reference is initialized
1555 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1556 be located centrally in the group. Using the COM from the
1557 previous step can be useful if one or more pull groups are large.
1559 .. mdp:: pull-xout-average
1563 Write the instantaneous coordinates for all the pulled groups.
1567 Write the average coordinates (since last output) for all the
1568 pulled groups. N.b., some analysis tools might expect instantaneous
1571 .. mdp:: pull-fout-average
1575 Write the instantaneous force for all the pulled groups.
1579 Write the average force (since last output) for all the
1580 pulled groups. N.b., some analysis tools might expect instantaneous
1583 .. mdp:: pull-ngroups
1586 The number of pull groups, not including the absolute reference
1587 group, when used. Pull groups can be reused in multiple pull
1588 coordinates. Below only the pull options for group 1 are given,
1589 further groups simply increase the group index number.
1591 .. mdp:: pull-ncoords
1594 The number of pull coordinates. Below only the pull options for
1595 coordinate 1 are given, further coordinates simply increase the
1596 coordinate index number.
1598 .. mdp:: pull-group1-name
1600 The name of the pull group, is looked up in the index file or in
1601 the default groups to obtain the atoms involved.
1603 .. mdp:: pull-group1-weights
1605 Optional relative weights which are multiplied with the masses of
1606 the atoms to give the total weight for the COM. The number should
1607 be 0, meaning all 1, or the number of atoms in the pull group.
1609 .. mdp:: pull-group1-pbcatom
1612 The reference atom for the treatment of periodic boundary
1613 conditions inside the group (this has no effect on the treatment of
1614 the pbc between groups). This option is only important when the
1615 diameter of the pull group is larger than half the shortest box
1616 vector. For determining the COM, all atoms in the group are put at
1617 their periodic image which is closest to
1618 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1619 atom (number wise) is used, which is only safe for small groups.
1620 :ref:`gmx grompp` checks that the maximum distance from the reference
1621 atom (specifically chosen, or not) to the other atoms in the group
1622 is not too large. This parameter is not used with
1623 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1624 weighting, which is useful for a group of molecules in a periodic
1625 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1628 .. mdp:: pull-coord1-type
1630 .. mdp-value:: umbrella
1632 Center of mass pulling using an umbrella potential between the
1633 reference group and one or more groups.
1635 .. mdp-value:: constraint
1637 Center of mass pulling using a constraint between the reference
1638 group and one or more groups. The setup is identical to the
1639 option umbrella, except for the fact that a rigid constraint is
1640 applied instead of a harmonic potential.
1642 .. mdp-value:: constant-force
1644 Center of mass pulling using a linear potential and therefore a
1645 constant force. For this option there is no reference position
1646 and therefore the parameters :mdp:`pull-coord1-init` and
1647 :mdp:`pull-coord1-rate` are not used.
1649 .. mdp-value:: flat-bottom
1651 At distances above :mdp:`pull-coord1-init` a harmonic potential
1652 is applied, otherwise no potential is applied.
1654 .. mdp-value:: flat-bottom-high
1656 At distances below :mdp:`pull-coord1-init` a harmonic potential
1657 is applied, otherwise no potential is applied.
1659 .. mdp-value:: external-potential
1661 An external potential that needs to be provided by another
1664 .. mdp:: pull-coord1-potential-provider
1666 The name of the external module that provides the potential for
1667 the case where :mdp:`pull-coord1-type` is external-potential.
1669 .. mdp:: pull-coord1-geometry
1671 .. mdp-value:: distance
1673 Pull along the vector connecting the two groups. Components can
1674 be selected with :mdp:`pull-coord1-dim`.
1676 .. mdp-value:: direction
1678 Pull in the direction of :mdp:`pull-coord1-vec`.
1680 .. mdp-value:: direction-periodic
1682 As :mdp-value:`pull-coord1-geometry=direction`, but does not apply
1683 periodic box vector corrections to keep the distance within half
1684 the box length. This is (only) useful for pushing groups apart
1685 by more than half the box length by continuously changing the reference
1686 location using a pull rate. With this geometry the box should not be
1687 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1688 the pull force is not added to the virial.
1690 .. mdp-value:: direction-relative
1692 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1693 that points from the COM of a third to the COM of a fourth pull
1694 group. This means that 4 groups need to be supplied in
1695 :mdp:`pull-coord1-groups`. Note that the pull force will give
1696 rise to a torque on the pull vector, which is turn leads to
1697 forces perpendicular to the pull vector on the two groups
1698 defining the vector. If you want a pull group to move between
1699 the two groups defining the vector, simply use the union of
1700 these two groups as the reference group.
1702 .. mdp-value:: cylinder
1704 Designed for pulling with respect to a layer where the reference
1705 COM is given by a local cylindrical part of the reference group.
1706 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1707 the first of the two groups in :mdp:`pull-coord1-groups` a
1708 cylinder is selected around the axis going through the COM of
1709 the second group with direction :mdp:`pull-coord1-vec` with
1710 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1711 continously to zero as the radial distance goes from 0 to
1712 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1713 dependence gives rise to radial forces on both pull groups.
1714 Note that the radius should be smaller than half the box size.
1715 For tilted cylinders they should be even smaller than half the
1716 box size since the distance of an atom in the reference group
1717 from the COM of the pull group has both a radial and an axial
1718 component. This geometry is not supported with constraint
1721 .. mdp-value:: angle
1723 Pull along an angle defined by four groups. The angle is
1724 defined as the angle between two vectors: the vector connecting
1725 the COM of the first group to the COM of the second group and
1726 the vector connecting the COM of the third group to the COM of
1729 .. mdp-value:: angle-axis
1731 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1732 Thus, only the two groups that define the first vector need to be given.
1734 .. mdp-value:: dihedral
1736 Pull along a dihedral angle defined by six groups. These pairwise
1737 define three vectors: the vector connecting the COM of group 1
1738 to the COM of group 2, the COM of group 3 to the COM of group 4,
1739 and the COM of group 5 to the COM group 6. The dihedral angle is
1740 then defined as the angle between two planes: the plane spanned by the
1741 the two first vectors and the plane spanned the two last vectors.
1744 .. mdp:: pull-coord1-groups
1746 The group indices on which this pull coordinate will operate.
1747 The number of group indices required is geometry dependent.
1748 The first index can be 0, in which case an
1749 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1750 absolute reference the system is no longer translation invariant
1751 and one should think about what to do with the center of mass
1754 .. mdp:: pull-coord1-dim
1757 Selects the dimensions that this pull coordinate acts on and that
1758 are printed to the output files when
1759 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1760 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1761 components set to Y contribute to the distance. Thus setting this
1762 to Y Y N results in a distance in the x/y plane. With other
1763 geometries all dimensions with non-zero entries in
1764 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1765 dimensions only affect the output.
1767 .. mdp:: pull-coord1-origin
1770 The pull reference position for use with an absolute reference.
1772 .. mdp:: pull-coord1-vec
1775 The pull direction. :ref:`gmx grompp` normalizes the vector.
1777 .. mdp:: pull-coord1-start
1781 do not modify :mdp:`pull-coord1-init`
1785 add the COM distance of the starting conformation to
1786 :mdp:`pull-coord1-init`
1788 .. mdp:: pull-coord1-init
1791 The reference distance or reference angle at t=0.
1793 .. mdp:: pull-coord1-rate
1795 (0) [nm/ps] or [deg/ps]
1796 The rate of change of the reference position or reference angle.
1798 .. mdp:: pull-coord1-k
1800 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1801 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1802 The force constant. For umbrella pulling this is the harmonic force
1803 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1804 for angles). For constant force pulling this is the
1805 force constant of the linear potential, and thus the negative (!)
1806 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1807 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1808 Note that for angles the force constant is expressed in terms of radians
1809 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1811 .. mdp:: pull-coord1-kB
1813 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1814 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1815 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1816 :mdp:`free-energy` is turned on. The force constant is then (1 -
1817 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1819 AWH adaptive biasing
1820 ^^^^^^^^^^^^^^^^^^^^
1830 Adaptively bias a reaction coordinate using the AWH method and estimate
1831 the corresponding PMF. The PMF and other AWH data are written to energy
1832 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1833 the ``gmx awh`` tool. The AWH coordinate can be
1834 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1835 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1836 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1837 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1839 .. mdp:: awh-potential
1841 .. mdp-value:: convolved
1843 The applied biasing potential is the convolution of the bias function and a
1844 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1845 in a smooth potential function and force. The resolution of the potential is set
1846 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1848 .. mdp-value:: umbrella
1850 The potential bias is applied by controlling the position of an harmonic potential
1851 using Monte-Carlo sampling. The force constant is set with
1852 :mdp:`awh1-dim1-force-constant`. The umbrella location
1853 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1854 There are no advantages to using an umbrella.
1855 This option is mainly for comparison and testing purposes.
1857 .. mdp:: awh-share-multisim
1861 AWH will not share biases across simulations started with
1862 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1866 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1867 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1868 with the biases with the same :mdp:`awh1-share-group` value.
1869 The simulations should have the same AWH settings for sharing to make sense.
1870 :ref:`gmx mdrun` will check whether the simulations are technically
1871 compatible for sharing, but the user should check that bias sharing
1872 physically makes sense.
1876 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1877 where -1 indicates to generate a seed. Only used with
1878 :mdp-value:`awh-potential=umbrella`.
1883 Number of steps between printing AWH data to the energy file, should be
1884 a multiple of :mdp:`nstenergy`.
1886 .. mdp:: awh-nstsample
1889 Number of steps between sampling of the coordinate value. This sampling
1890 is the basis for updating the bias and estimating the PMF and other AWH observables.
1892 .. mdp:: awh-nsamples-update
1895 The number of coordinate samples used for each AWH update.
1896 The update interval in steps is :mdp:`awh-nstsample` times this value.
1901 The number of biases, each acting on its own coordinate.
1902 The following options should be specified
1903 for each bias although below only the options for bias number 1 is shown. Options for
1904 other bias indices are obtained by replacing '1' by the bias index.
1906 .. mdp:: awh1-error-init
1908 (10.0) [kJ mol\ :sup:`-1`]
1909 Estimated initial average error of the PMF for this bias. This value together with the
1910 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1911 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1913 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1914 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1915 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1916 then :mdp:`awh1-error-init` should reflect that knowledge.
1918 .. mdp:: awh1-growth
1920 .. mdp-value:: exp-linear
1922 Each bias keeps a reference weight histogram for the coordinate samples.
1923 Its size sets the magnitude of the bias function and free energy estimate updates
1924 (few samples corresponds to large updates and vice versa).
1925 Thus, its growth rate sets the maximum convergence rate.
1926 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1927 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1928 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1929 high free energy barriers have not yet been flattened by the bias.
1931 .. mdp-value:: linear
1933 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1934 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
1935 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
1937 .. mdp:: awh1-equilibrate-histogram
1941 Do not equilibrate histogram.
1945 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
1946 histogram of sampled weights is following the target distribution closely enough (specifically,
1947 at least 80% of the target region needs to have a local relative error of less than 20%). This
1948 option would typically only be used when :mdp:`awh1-share-group` > 0
1949 and the initial configurations poorly represent the target
1952 .. mdp:: awh1-target
1954 .. mdp-value:: constant
1956 The bias is tuned towards a constant (uniform) coordinate distribution
1957 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
1959 .. mdp-value:: cutoff
1961 Similar to :mdp-value:`awh1-target=constant`, but the target
1962 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
1963 where F is the free energy relative to the estimated global minimum.
1964 This provides a smooth switch of a flat target distribution in
1965 regions with free energy lower than the cut-off to a Boltzmann
1966 distribution in regions with free energy higher than the cut-off.
1968 .. mdp-value:: boltzmann
1970 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
1971 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
1972 would give the same coordinate distribution as sampling with a simulation temperature
1975 .. mdp-value:: local-boltzmann
1977 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
1978 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
1979 change of the bias only depends on the local sampling. This local convergence property is
1980 only compatible with :mdp-value:`awh1-growth=linear`, since for
1981 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
1983 .. mdp:: awh1-target-beta-scaling
1986 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
1987 it is the unitless beta scaling factor taking values in (0,1).
1989 .. mdp:: awh1-target-cutoff
1991 (0) [kJ mol\ :sup:`-1`]
1992 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
1994 .. mdp:: awh1-user-data
1998 Initialize the PMF and target distribution with default values.
2002 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2003 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2004 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2005 The file name can be changed with the ``-awh`` option.
2006 The first :mdp:`awh1-ndim` columns of
2007 each input file should contain the coordinate values, such that each row defines a point in
2008 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
2009 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2010 be in the same column as written by :ref:`gmx awh`.
2012 .. mdp:: awh1-share-group
2016 Do not share the bias.
2018 .. mdp-value:: positive
2020 Share the bias and PMF estimates within and/or between simulations.
2021 Within a simulation, the bias will be shared between biases that have the
2022 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2023 With :mdp-value:`awh-share-multisim=yes` and
2024 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2025 Sharing may increase convergence initially, although the starting configurations
2026 can be critical, especially when sharing between many biases.
2027 Currently, positive group values should start at 1 and increase
2028 by 1 for each subsequent bias that is shared.
2033 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2034 The following options should be specified for each such dimension. Below only
2035 the options for dimension number 1 is shown. Options for other dimension indices are
2036 obtained by replacing '1' by the dimension index.
2038 .. mdp:: awh1-dim1-coord-provider
2042 The module providing the reaction coordinate for this dimension.
2043 Currently AWH can only act on pull coordinates.
2045 .. mdp:: awh1-dim1-coord-index
2048 Index of the pull coordinate defining this coordinate dimension.
2050 .. mdp:: awh1-dim1-force-constant
2052 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2053 Force constant for the (convolved) umbrella potential(s) along this
2054 coordinate dimension.
2056 .. mdp:: awh1-dim1-start
2059 Start value of the sampling interval along this dimension. The range of allowed
2060 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2061 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2062 is allowed. The interval will then wrap around from +period/2 to -period/2.
2063 For the direction geometry, the dimension is made periodic when
2064 the direction is along a box vector and covers more than 95%
2065 of the box length. Note that one should not apply pressure coupling
2066 along a periodic dimension.
2068 .. mdp:: awh1-dim1-end
2071 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2073 .. mdp:: awh1-dim1-diffusion
2075 (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps]
2076 Estimated diffusion constant for this coordinate dimension determining the initial
2077 biasing rate. This needs only be a rough estimate and should not critically
2078 affect the results unless it is set to something very low, leading to slow convergence,
2079 or very high, forcing the system far from equilibrium. Not setting this value
2080 explicitly generates a warning.
2082 .. mdp:: awh1-dim1-cover-diameter
2085 Diameter that needs to be sampled by a single simulation around a coordinate value
2086 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2087 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2088 across each coordinate value.
2089 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2090 (:mdp:`awh1-share-group`>0).
2091 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2092 for many sharing simulations does not guarantee transitions across free energy barriers.
2093 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2094 has independently sampled the whole interval.
2099 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2100 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2101 that can be used to achieve such a rotation.
2107 No enforced rotation will be applied. All enforced rotation options will
2108 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2113 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2114 under the :mdp:`rot-group0` option.
2116 .. mdp:: rot-ngroups
2119 Number of rotation groups.
2123 Name of rotation group 0 in the index file.
2128 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2129 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2130 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2135 Use mass weighted rotation group positions.
2140 Rotation vector, will get normalized.
2145 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2149 (0) [degree ps\ :sup:`-1`]
2150 Reference rotation rate of group 0.
2154 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2155 Force constant for group 0.
2157 .. mdp:: rot-slab-dist0
2160 Slab distance, if a flexible axis rotation type was chosen.
2162 .. mdp:: rot-min-gauss0
2165 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2166 (for the flexible axis potentials).
2170 (0.0001) [nm\ :sup:`2`]
2171 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2173 .. mdp:: rot-fit-method0
2176 Fitting method when determining the actual angle of a rotation group
2177 (can be one of ``rmsd``, ``norm``, or ``potential``).
2179 .. mdp:: rot-potfit-nsteps0
2182 For fit type ``potential``, the number of angular positions around the reference angle for which the
2183 rotation potential is evaluated.
2185 .. mdp:: rot-potfit-step0
2188 For fit type ``potential``, the distance in degrees between two angular positions.
2190 .. mdp:: rot-nstrout
2193 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2194 and the rotation potential energy.
2196 .. mdp:: rot-nstsout
2199 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2209 ignore distance restraint information in topology file
2211 .. mdp-value:: simple
2213 simple (per-molecule) distance restraints.
2215 .. mdp-value:: ensemble
2217 distance restraints over an ensemble of molecules in one
2218 simulation box. Normally, one would perform ensemble averaging
2219 over multiple simulations, using ``mdrun
2220 -multidir``. The environment
2221 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2222 within each ensemble (usually equal to the number of directories
2223 supplied to ``mdrun -multidir``).
2225 .. mdp:: disre-weighting
2227 .. mdp-value:: equal
2229 divide the restraint force equally over all atom pairs in the
2232 .. mdp-value:: conservative
2234 the forces are the derivative of the restraint potential, this
2235 results in an weighting of the atom pairs to the reciprocal
2236 seventh power of the displacement. The forces are conservative
2237 when :mdp:`disre-tau` is zero.
2239 .. mdp:: disre-mixed
2243 the violation used in the calculation of the restraint force is
2244 the time-averaged violation
2248 the violation used in the calculation of the restraint force is
2249 the square root of the product of the time-averaged violation
2250 and the instantaneous violation
2254 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2255 force constant for distance restraints, which is multiplied by a
2256 (possibly) different factor for each restraint given in the ``fac``
2257 column of the interaction in the topology file.
2262 time constant for distance restraints running average. A value of
2263 zero turns off time averaging.
2265 .. mdp:: nstdisreout
2268 period between steps when the running time-averaged and
2269 instantaneous distances of all atom pairs involved in restraints
2270 are written to the energy file (can make the energy file very
2277 ignore orientation restraint information in topology file
2281 use orientation restraints, ensemble averaging can be performed
2282 with ``mdrun -multidir``
2286 (0) [kJ mol\ :sup:`-1`]
2287 force constant for orientation restraints, which is multiplied by a
2288 (possibly) different weight factor for each restraint, can be set
2289 to zero to obtain the orientations from a free simulation
2294 time constant for orientation restraints running average. A value
2295 of zero turns off time averaging.
2297 .. mdp:: orire-fitgrp
2299 fit group for orientation restraining. This group of atoms is used
2300 to determine the rotation **R** of the system with respect to the
2301 reference orientation. The reference orientation is the starting
2302 conformation of the first subsystem. For a protein, backbone is a
2305 .. mdp:: nstorireout
2308 period between steps when the running time-averaged and
2309 instantaneous orientations for all restraints, and the molecular
2310 order tensor are written to the energy file (can make the energy
2314 Free energy calculations
2315 ^^^^^^^^^^^^^^^^^^^^^^^^
2317 .. mdp:: free-energy
2321 Only use topology A.
2325 Interpolate between topology A (lambda=0) to topology B
2326 (lambda=1) and write the derivative of the Hamiltonian with
2327 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2328 or the Hamiltonian differences with respect to other lambda
2329 values (as specified with foreign lambda) to the energy file
2330 and/or to ``dhdl.xvg``, where they can be processed by, for
2331 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2332 are interpolated linearly as described in the manual. When
2333 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2334 used for the LJ and Coulomb interactions.
2338 Turns on expanded ensemble simulation, where the alchemical state
2339 becomes a dynamic variable, allowing jumping between different
2340 Hamiltonians. See the expanded ensemble options for controlling how
2341 expanded ensemble simulations are performed. The different
2342 Hamiltonians used in expanded ensemble simulations are defined by
2343 the other free energy options.
2345 .. mdp:: init-lambda
2348 starting value for lambda (float). Generally, this should only be
2349 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2350 other cases, :mdp:`init-lambda-state` should be specified
2351 instead. Must be greater than or equal to 0.
2353 .. mdp:: delta-lambda
2356 increment per time step for lambda
2358 .. mdp:: init-lambda-state
2361 starting value for the lambda state (integer). Specifies which
2362 columm of the lambda vector (:mdp:`coul-lambdas`,
2363 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2364 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2365 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2366 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2367 the first column, and so on.
2369 .. mdp:: fep-lambdas
2372 Zero, one or more lambda values for which Delta H values will be
2373 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2374 steps. Values must be between 0 and 1. Free energy differences
2375 between different lambda values can then be determined with
2376 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2377 other -lambdas keywords because all components of the lambda vector
2378 that are not specified will use :mdp:`fep-lambdas` (including
2379 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2381 .. mdp:: coul-lambdas
2384 Zero, one or more lambda values for which Delta H values will be
2385 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2386 steps. Values must be between 0 and 1. Only the electrostatic
2387 interactions are controlled with this component of the lambda
2388 vector (and only if the lambda=0 and lambda=1 states have differing
2389 electrostatic interactions).
2391 .. mdp:: vdw-lambdas
2394 Zero, one or more lambda values for which Delta H values will be
2395 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2396 steps. Values must be between 0 and 1. Only the van der Waals
2397 interactions are controlled with this component of the lambda
2400 .. mdp:: bonded-lambdas
2403 Zero, one or more lambda values for which Delta H values will be
2404 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2405 steps. Values must be between 0 and 1. Only the bonded interactions
2406 are controlled with this component of the lambda vector.
2408 .. mdp:: restraint-lambdas
2411 Zero, one or more lambda values for which Delta H values will be
2412 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2413 steps. Values must be between 0 and 1. Only the restraint
2414 interactions: dihedral restraints, and the pull code restraints are
2415 controlled with this component of the lambda vector.
2417 .. mdp:: mass-lambdas
2420 Zero, one or more lambda values for which Delta H values will be
2421 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2422 steps. Values must be between 0 and 1. Only the particle masses are
2423 controlled with this component of the lambda vector.
2425 .. mdp:: temperature-lambdas
2428 Zero, one or more lambda values for which Delta H values will be
2429 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2430 steps. Values must be between 0 and 1. Only the temperatures
2431 controlled with this component of the lambda vector. Note that
2432 these lambdas should not be used for replica exchange, only for
2433 simulated tempering.
2435 .. mdp:: calc-lambda-neighbors
2438 Controls the number of lambda values for which Delta H values will
2439 be calculated and written out, if :mdp:`init-lambda-state` has
2440 been set. A positive value will limit the number of lambda points
2441 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2442 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2443 has a value of 2, energies for lambda points 3-7 will be calculated
2444 and writen out. A value of -1 means all lambda points will be
2445 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2446 1 is sufficient, while for MBAR -1 should be used.
2451 the soft-core alpha parameter, a value of 0 results in linear
2452 interpolation of the LJ and Coulomb interactions
2457 power 6 for the radial term in the soft-core equation.
2460 (deprecated) power 48 for the radial term in the soft-core equation.
2461 Note that sc-alpha should generally be much lower (between 0.001 and 0.003).
2466 Whether to apply the soft-core free energy interaction
2467 transformation to the Columbic interaction of a molecule. Default
2468 is no, as it is generally more efficient to turn off the Coulomic
2469 interactions linearly before turning off the van der Waals
2470 interactions. Note that it is only taken into account when lambda
2471 states are used, not with :mdp:`couple-lambda0` /
2472 :mdp:`couple-lambda1`, and you can still turn off soft-core
2473 interactions by setting :mdp:`sc-alpha` to 0.
2478 the power for lambda in the soft-core function, only the values 1
2484 the soft-core sigma for particles which have a C6 or C12 parameter
2485 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2487 .. mdp:: couple-moltype
2489 Here one can supply a molecule type (as defined in the topology)
2490 for calculating solvation or coupling free energies. There is a
2491 special option ``system`` that couples all molecule types in the
2492 system. This can be useful for equilibrating a system starting from
2493 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2494 on. The Van der Waals interactions and/or charges in this molecule
2495 type can be turned on or off between lambda=0 and lambda=1,
2496 depending on the settings of :mdp:`couple-lambda0` and
2497 :mdp:`couple-lambda1`. If you want to decouple one of several
2498 copies of a molecule, you need to copy and rename the molecule
2499 definition in the topology.
2501 .. mdp:: couple-lambda0
2503 .. mdp-value:: vdw-q
2505 all interactions are on at lambda=0
2509 the charges are zero (no Coulomb interactions) at lambda=0
2513 the Van der Waals interactions are turned at lambda=0; soft-core
2514 interactions will be required to avoid singularities
2518 the Van der Waals interactions are turned off and the charges
2519 are zero at lambda=0; soft-core interactions will be required to
2520 avoid singularities.
2522 .. mdp:: couple-lambda1
2524 analogous to :mdp:`couple-lambda1`, but for lambda=1
2526 .. mdp:: couple-intramol
2530 All intra-molecular non-bonded interactions for moleculetype
2531 :mdp:`couple-moltype` are replaced by exclusions and explicit
2532 pair interactions. In this manner the decoupled state of the
2533 molecule corresponds to the proper vacuum state without
2534 periodicity effects.
2538 The intra-molecular Van der Waals and Coulomb interactions are
2539 also turned on/off. This can be useful for partitioning
2540 free-energies of relatively large molecules, where the
2541 intra-molecular non-bonded interactions might lead to
2542 kinetically trapped vacuum conformations. The 1-4 pair
2543 interactions are not turned off.
2548 the frequency for writing dH/dlambda and possibly Delta H to
2549 dhdl.xvg, 0 means no ouput, should be a multiple of
2550 :mdp:`nstcalcenergy`.
2552 .. mdp:: dhdl-derivatives
2556 If yes (the default), the derivatives of the Hamiltonian with
2557 respect to lambda at each :mdp:`nstdhdl` step are written
2558 out. These values are needed for interpolation of linear energy
2559 differences with :ref:`gmx bar` (although the same can also be
2560 achieved with the right foreign lambda setting, that may not be as
2561 flexible), or with thermodynamic integration
2563 .. mdp:: dhdl-print-energy
2567 Include either the total or the potential energy in the dhdl
2568 file. Options are 'no', 'potential', or 'total'. This information
2569 is needed for later free energy analysis if the states of interest
2570 are at different temperatures. If all states are at the same
2571 temperature, this information is not needed. 'potential' is useful
2572 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2573 file. When rerunning from an existing trajectory, the kinetic
2574 energy will often not be correct, and thus one must compute the
2575 residual free energy from the potential alone, with the kinetic
2576 energy component computed analytically.
2578 .. mdp:: separate-dhdl-file
2582 The free energy values that are calculated (as specified with
2583 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2584 written out to a separate file, with the default name
2585 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2590 The free energy values are written out to the energy output file
2591 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2592 steps), where they can be extracted with :ref:`gmx energy` or
2593 used directly with :ref:`gmx bar`.
2595 .. mdp:: dh-hist-size
2598 If nonzero, specifies the size of the histogram into which the
2599 Delta H values (specified with foreign lambda) and the derivative
2600 dH/dl values are binned, and written to ener.edr. This can be used
2601 to save disk space while calculating free energy differences. One
2602 histogram gets written for each foreign lambda and two for the
2603 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2604 histogram settings (too small size or too wide bins) can introduce
2605 errors. Do not use histograms unless you're certain you need it.
2607 .. mdp:: dh-hist-spacing
2610 Specifies the bin width of the histograms, in energy units. Used in
2611 conjunction with :mdp:`dh-hist-size`. This size limits the
2612 accuracy with which free energies can be calculated. Do not use
2613 histograms unless you're certain you need it.
2616 Expanded Ensemble calculations
2617 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2619 .. mdp:: nstexpanded
2621 The number of integration steps beween attempted moves changing the
2622 system Hamiltonian in expanded ensemble simulations. Must be a
2623 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2630 No Monte Carlo in state space is performed.
2632 .. mdp-value:: metropolis-transition
2634 Uses the Metropolis weights to update the expanded ensemble
2635 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2638 .. mdp-value:: barker-transition
2640 Uses the Barker transition critera to update the expanded
2641 ensemble weight of each state i, defined by exp(-beta_new
2642 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2644 .. mdp-value:: wang-landau
2646 Uses the Wang-Landau algorithm (in state space, not energy
2647 space) to update the expanded ensemble weights.
2649 .. mdp-value:: min-variance
2651 Uses the minimum variance updating method of Escobedo et al. to
2652 update the expanded ensemble weights. Weights will not be the
2653 free energies, but will rather emphasize states that need more
2654 sampling to give even uncertainty.
2656 .. mdp:: lmc-mc-move
2660 No Monte Carlo in state space is performed.
2662 .. mdp-value:: metropolis-transition
2664 Randomly chooses a new state up or down, then uses the
2665 Metropolis critera to decide whether to accept or reject:
2666 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2668 .. mdp-value:: barker-transition
2670 Randomly chooses a new state up or down, then uses the Barker
2671 transition critera to decide whether to accept or reject:
2672 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2674 .. mdp-value:: gibbs
2676 Uses the conditional weights of the state given the coordinate
2677 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2680 .. mdp-value:: metropolized-gibbs
2682 Uses the conditional weights of the state given the coordinate
2683 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2684 to move to, EXCLUDING the current state, then uses a rejection
2685 step to ensure detailed balance. Always more efficient that
2686 Gibbs, though only marginally so in many situations, such as
2687 when only the nearest neighbors have decent phase space
2693 random seed to use for Monte Carlo moves in state space. When
2694 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2696 .. mdp:: mc-temperature
2698 Temperature used for acceptance/rejection for Monte Carlo moves. If
2699 not specified, the temperature of the simulation specified in the
2700 first group of :mdp:`ref-t` is used.
2705 The cutoff for the histogram of state occupancies to be reset, and
2706 the free energy incrementor to be changed from delta to delta *
2707 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2708 each histogram) / (average number of samples at each
2709 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2710 histogram is only considered flat if all Nratio > 0.8 AND
2711 simultaneously all 1/Nratio > 0.8.
2716 Each time the histogram is considered flat, then the current value
2717 of the Wang-Landau incrementor for the free energies is multiplied
2718 by :mdp:`wl-scale`. Value must be between 0 and 1.
2720 .. mdp:: init-wl-delta
2723 The initial value of the Wang-Landau incrementor in kT. Some value
2724 near 1 kT is usually most efficient, though sometimes a value of
2725 2-3 in units of kT works better if the free energy differences are
2728 .. mdp:: wl-oneovert
2731 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2732 the large sample limit. There is significant evidence that the
2733 standard Wang-Landau algorithms in state space presented here
2734 result in free energies getting 'burned in' to incorrect values
2735 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2736 then when the incrementor becomes less than 1/N, where N is the
2737 mumber of samples collected (and thus proportional to the data
2738 collection time, hence '1 over t'), then the Wang-Lambda
2739 incrementor is set to 1/N, decreasing every step. Once this occurs,
2740 :mdp:`wl-ratio` is ignored, but the weights will still stop
2741 updating when the equilibration criteria set in
2742 :mdp:`lmc-weights-equil` is achieved.
2744 .. mdp:: lmc-repeats
2747 Controls the number of times that each Monte Carlo swap type is
2748 performed each iteration. In the limit of large numbers of Monte
2749 Carlo repeats, then all methods converge to Gibbs sampling. The
2750 value will generally not need to be different from 1.
2752 .. mdp:: lmc-gibbsdelta
2755 Limit Gibbs sampling to selected numbers of neighboring states. For
2756 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2757 sampling over all of the states that are defined. A positive value
2758 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2759 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2760 value of -1 means that all states are considered. For less than 100
2761 states, it is probably not that expensive to include all states.
2763 .. mdp:: lmc-forced-nstart
2766 Force initial state space sampling to generate weights. In order to
2767 come up with reasonable initial weights, this setting allows the
2768 simulation to drive from the initial to the final lambda state,
2769 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2770 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2771 sufficiently long (thousands of steps, perhaps), then the weights
2772 will be close to correct. However, in most cases, it is probably
2773 better to simply run the standard weight equilibration algorithms.
2775 .. mdp:: nst-transition-matrix
2778 Frequency of outputting the expanded ensemble transition matrix. A
2779 negative number means it will only be printed at the end of the
2782 .. mdp:: symmetrized-transition-matrix
2785 Whether to symmetrize the empirical transition matrix. In the
2786 infinite limit the matrix will be symmetric, but will diverge with
2787 statistical noise for short timescales. Forced symmetrization, by
2788 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2789 like the existence of (small magnitude) negative eigenvalues.
2791 .. mdp:: mininum-var-min
2794 The min-variance strategy (option of :mdp:`lmc-stats` is only
2795 valid for larger number of samples, and can get stuck if too few
2796 samples are used at each state. :mdp:`mininum-var-min` is the
2797 minimum number of samples that each state that are allowed before
2798 the min-variance strategy is activated if selected.
2800 .. mdp:: init-lambda-weights
2802 The initial weights (free energies) used for the expanded ensemble
2803 states. Default is a vector of zero weights. format is similar to
2804 the lambda vector settings in :mdp:`fep-lambdas`, except the
2805 weights can be any floating point number. Units are kT. Its length
2806 must match the lambda vector lengths.
2808 .. mdp:: lmc-weights-equil
2812 Expanded ensemble weights continue to be updated throughout the
2817 The input expanded ensemble weights are treated as equilibrated,
2818 and are not updated throughout the simulation.
2820 .. mdp-value:: wl-delta
2822 Expanded ensemble weight updating is stopped when the
2823 Wang-Landau incrementor falls below this value.
2825 .. mdp-value:: number-all-lambda
2827 Expanded ensemble weight updating is stopped when the number of
2828 samples at all of the lambda states is greater than this value.
2830 .. mdp-value:: number-steps
2832 Expanded ensemble weight updating is stopped when the number of
2833 steps is greater than the level specified by this value.
2835 .. mdp-value:: number-samples
2837 Expanded ensemble weight updating is stopped when the number of
2838 total samples across all lambda states is greater than the level
2839 specified by this value.
2841 .. mdp-value:: count-ratio
2843 Expanded ensemble weight updating is stopped when the ratio of
2844 samples at the least sampled lambda state and most sampled
2845 lambda state greater than this value.
2847 .. mdp:: simulated-tempering
2850 Turn simulated tempering on or off. Simulated tempering is
2851 implemented as expanded ensemble sampling with different
2852 temperatures instead of different Hamiltonians.
2854 .. mdp:: sim-temp-low
2857 Low temperature for simulated tempering.
2859 .. mdp:: sim-temp-high
2862 High temperature for simulated tempering.
2864 .. mdp:: simulated-tempering-scaling
2866 Controls the way that the temperatures at intermediate lambdas are
2867 calculated from the :mdp:`temperature-lambdas` part of the lambda
2870 .. mdp-value:: linear
2872 Linearly interpolates the temperatures using the values of
2873 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2874 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2875 a temperature of 350. A nonlinear set of temperatures can always
2876 be implemented with uneven spacing in lambda.
2878 .. mdp-value:: geometric
2880 Interpolates temperatures geometrically between
2881 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2882 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2883 :mdp:`sim-temp-low`) raised to the power of
2884 (i/(ntemps-1)). This should give roughly equal exchange for
2885 constant heat capacity, though of course things simulations that
2886 involve protein folding have very high heat capacity peaks.
2888 .. mdp-value:: exponential
2890 Interpolates temperatures exponentially between
2891 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2892 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2893 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2894 (i))-1)/(exp(1.0)-i)).
2902 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2903 in groups Protein and Sol will experience constant acceleration as
2904 specified in the :mdp:`accelerate` line
2908 (0) [nm ps\ :sup:`-2`]
2909 acceleration for :mdp:`acc-grps`; x, y and z for each group
2910 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2911 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
2916 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2917 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2918 specifies for which dimension(s) the freezing applies. To avoid
2919 spurious contributions to the virial and pressure due to large
2920 forces between completely frozen atoms you need to use energy group
2921 exclusions, this also saves computing time. Note that coordinates
2922 of frozen atoms are not scaled by pressure-coupling algorithms.
2926 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2927 specify ``Y`` or ``N`` for X, Y and Z and for each group (*e.g.*
2928 ``Y Y N N N N`` means that particles in the first group can move only in
2929 Z direction. The particles in the second group can move in any
2932 .. mdp:: cos-acceleration
2934 (0) [nm ps\ :sup:`-2`]
2935 the amplitude of the acceleration profile for calculating the
2936 viscosity. The acceleration is in the X-direction and the magnitude
2937 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2938 added to the energy file: the amplitude of the velocity profile and
2943 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
2944 The velocities of deformation for the box elements: a(x) b(y) c(z)
2945 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2946 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2947 elements are corrected for periodicity. The coordinates are
2948 transformed accordingly. Frozen degrees of freedom are (purposely)
2949 also transformed. The time ts is set to t at the first step and at
2950 steps at which x and v are written to trajectory to ensure exact
2951 restarts. Deformation can be used together with semiisotropic or
2952 anisotropic pressure coupling when the appropriate
2953 compressibilities are set to zero. The diagonal elements can be
2954 used to strain a solid. The off-diagonal elements can be used to
2955 shear a solid or a liquid.
2961 .. mdp:: electric-field-x
2962 .. mdp:: electric-field-y
2963 .. mdp:: electric-field-z
2965 Here you can specify an electric field that optionally can be
2966 alternating and pulsed. The general expression for the field
2967 has the form of a gaussian laser pulse:
2969 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
2971 For example, the four parameters for direction x are set in the
2972 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
2973 and ``electric-field-z``) like
2975 ``electric-field-x = E0 omega t0 sigma``
2977 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
2979 In the special case that ``sigma = 0``, the exponential term is omitted
2980 and only the cosine term is used. If also ``omega = 0`` a static
2981 electric field is applied.
2983 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
2986 Mixed quantum/classical molecular dynamics
2987 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2997 Do a QM/MM simulation. Several groups can be described at
2998 different QM levels separately. These are specified in the
2999 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
3000 initio* theory at which the groups are described is specified by
3001 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
3002 groups at different levels of theory is only possible with the
3003 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
3007 groups to be descibed at the QM level (works also in case of MiMiC QM/MM)
3011 .. mdp-value:: normal
3013 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
3014 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
3015 *ab initio* theory. The rest of the system is described at the
3016 MM level. The QM and MM subsystems interact as follows: MM point
3017 charges are included in the QM one-electron hamiltonian and all
3018 Lennard-Jones interactions are described at the MM level.
3020 .. mdp-value:: ONIOM
3022 The interaction between the subsystem is described using the
3023 ONIOM method by Morokuma and co-workers. There can be more than
3024 one :mdp:`QMMM-grps` each modeled at a different level of QM
3025 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
3030 Method used to compute the energy and gradients on the QM
3031 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
3032 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
3033 included in the active space is specified by :mdp:`CASelectrons`
3034 and :mdp:`CASorbitals`.
3039 Basis set used to expand the electronic wavefuntion. Only Gaussian
3040 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3041 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
3046 The total charge in ``e`` of the :mdp:`QMMM-grps`. In case there are
3047 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
3048 layer needs to be specified separately.
3053 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
3054 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
3055 needs to be specified separately.
3057 .. mdp:: CASorbitals
3060 The number of orbitals to be included in the active space when
3061 doing a CASSCF computation.
3063 .. mdp:: CASelectrons
3066 The number of electrons to be included in the active space when
3067 doing a CASSCF computation.
3073 No surface hopping. The system is always in the electronic
3078 Do a QM/MM MD simulation on the excited state-potential energy
3079 surface and enforce a *diabatic* hop to the ground-state when
3080 the system hits the conical intersection hyperline in the course
3081 the simulation. This option only works in combination with the
3085 Computational Electrophysiology
3086 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3087 Use these options to switch on and control ion/water position exchanges in "Computational
3088 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3094 Do not enable ion/water position exchanges.
3096 .. mdp-value:: X ; Y ; Z
3098 Allow for ion/water position exchanges along the chosen direction.
3099 In a typical setup with the membranes parallel to the x-y plane,
3100 ion/water pairs need to be exchanged in Z direction to sustain the
3101 requested ion concentrations in the compartments.
3103 .. mdp:: swap-frequency
3105 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3106 per compartment are determined and exchanges made if necessary.
3107 Normally it is not necessary to check at every time step.
3108 For typical Computational Electrophysiology setups, a value of about 100 is
3109 sufficient and yields a negligible performance impact.
3111 .. mdp:: split-group0
3113 Name of the index group of the membrane-embedded part of channel #0.
3114 The center of mass of these atoms defines one of the compartment boundaries
3115 and should be chosen such that it is near the center of the membrane.
3117 .. mdp:: split-group1
3119 Channel #1 defines the position of the other compartment boundary.
3121 .. mdp:: massw-split0
3123 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3127 Use the geometrical center.
3131 Use the center of mass.
3133 .. mdp:: massw-split1
3135 (no) As above, but for split-group #1.
3137 .. mdp:: solvent-group
3139 Name of the index group of solvent molecules.
3141 .. mdp:: coupl-steps
3143 (10) Average the number of ions per compartment over these many swap attempt steps.
3144 This can be used to prevent that ions near a compartment boundary
3145 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3149 (1) The number of different ion types to be controlled. These are during the
3150 simulation exchanged with solvent molecules to reach the desired reference numbers.
3152 .. mdp:: iontype0-name
3154 Name of the first ion type.
3156 .. mdp:: iontype0-in-A
3158 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3159 The default value of -1 means: use the number of ions as found in time step 0
3162 .. mdp:: iontype0-in-B
3164 (-1) Reference number of ions of type 0 for compartment B.
3166 .. mdp:: bulk-offsetA
3168 (0.0) Offset of the first swap layer from the compartment A midplane.
3169 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3170 at maximum distance (= bulk concentration) to the split group layers. However,
3171 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3172 towards one of the compartment-partitioning layers (at +/- 1.0).
3174 .. mdp:: bulk-offsetB
3176 (0.0) Offset of the other swap layer from the compartment B midplane.
3181 (\1) Only swap ions if threshold difference to requested count is reached.
3185 (2.0) [nm] Radius of the split cylinder #0.
3186 Two split cylinders (mimicking the channel pores) can optionally be defined
3187 relative to the center of the split group. With the help of these cylinders
3188 it can be counted which ions have passed which channel. The split cylinder
3189 definition has no impact on whether or not ion/water swaps are done.
3193 (1.0) [nm] Upper extension of the split cylinder #0.
3197 (1.0) [nm] Lower extension of the split cylinder #0.
3201 (2.0) [nm] Radius of the split cylinder #1.
3205 (1.0) [nm] Upper extension of the split cylinder #1.
3209 (1.0) [nm] Lower extension of the split cylinder #1.
3211 Density-guided simulations
3212 ^^^^^^^^^^^^^^^^^^^^^^^^^^
3214 These options enable and control the calculation and application of additional
3215 forces that are derived from three-dimensional densities, e.g., from cryo
3216 electron-microscopy experiments. (See the `reference manual`_ for details)
3218 .. mdp:: density-guided-simulation-active
3220 (no) Activate density-guided simulations.
3222 .. mdp:: density-guided-simulation-group
3224 (protein) The atoms that are subject to the forces from the density-guided
3225 simulation and contribute to the simulated density.
3227 .. mdp:: density-guided-simulation-similarity-measure
3229 (inner-product) Similarity measure between the density that is calculated
3230 from the atom positions and the reference density.
3232 .. mdp-value:: inner-product
3234 Takes the sum of the product of reference density and simulated density
3237 .. mdp-value:: relative-entropy
3239 Uses the negative relative entropy (or Kullback-Leibler divergence)
3240 between reference density and simulated density as similarity measure.
3241 Negative density values are ignored.
3243 .. mdp:: density-guided-simulation-atom-spreading-weight
3245 (unity) Determines the multiplication factor for the Gaussian kernel when
3246 spreading atoms on the grid.
3248 .. mdp-value:: unity
3250 Every atom in the density fitting group is assigned the same unit factor.
3254 Atoms contribute to the simulated density proportional to their mass.
3256 .. mdp-value:: charge
3258 Atoms contribute to the simulated density proportional to their charge.
3260 .. mdp:: density-guided-simulation-force-constant
3262 (1e+09) [kJ mol\ :sup:`-1`] The scaling factor for density-guided simulation
3263 forces. May also be negative.
3265 .. mdp:: density-guided-simulation-gaussian-transform-spreading-width
3267 (0.2) [nm] The Gaussian RMS width for the spread kernel for the simulated
3270 .. mdp:: density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width
3272 (4) The range after which the gaussian is cut off in multiples of the Gaussian
3273 RMS width described above.
3275 .. mdp:: density-guided-simulation-reference-density-filename
3277 (reference.mrc) Reference density file name using an absolute path or a path
3278 relative to the to the folder from which :ref:`gmx mdrun` is called.
3280 .. mdp:: density-guided-simulation-nst
3282 (1) Interval in steps at which the density fitting forces are evaluated
3283 and applied. The forces are scaled by this number when applied (See the
3284 `reference manual`_ for details).
3286 .. mdp:: density-guided-simulation-normalize-densities
3288 (true) Normalize the sum of density voxel values to one for the reference
3289 density as well as the simulated density.
3291 .. mdp:: density-guided-simulation-adaptive-force-scaling
3293 (false) Adapt the force constant to ensure a steady increase in similarity
3294 between simulated and reference density.
3298 Do not use adaptive force scaling.
3302 Use adaptive force scaling.
3304 .. mdp:: density-guided-simulation-adaptive-force-scaling-time-constant
3306 (4) [ps] Couple force constant to increase in similarity with reference density
3307 with this time constant. Larger times result in looser coupling.
3309 User defined thingies
3310 ^^^^^^^^^^^^^^^^^^^^^
3314 .. mdp:: userint1 (0)
3315 .. mdp:: userint2 (0)
3316 .. mdp:: userint3 (0)
3317 .. mdp:: userint4 (0)
3318 .. mdp:: userreal1 (0)
3319 .. mdp:: userreal2 (0)
3320 .. mdp:: userreal3 (0)
3321 .. mdp:: userreal4 (0)
3323 These you can use if you modify code. You can pass integers and
3324 reals and groups to your subroutine. Check the inputrec definition
3325 in ``src/gromacs/mdtypes/inputrec.h``
3330 These features have been removed from |Gromacs|, but so that old
3331 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3332 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3333 fatal error if this is set.
3339 .. mdp:: implicit-solvent
3343 .. _reference manual: gmx-manual-parent-dir_