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 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 parameter :mdp:`tcoupl` is
98 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
365 number of steps that elapse between writing velocities to the output
366 trajectory file (:ref:`trr`), the last velocities are always written
371 number of steps that elapse between writing forces to the output
372 trajectory file (:ref:`trr`), the last forces are always written.
377 number of steps that elapse between writing energies to the log
378 file, the last energies are always written
380 .. mdp:: nstcalcenergy
383 number of steps that elapse between calculating the energies, 0 is
384 never. This option is only relevant with dynamics. This option affects the
385 performance in parallel simulations, because calculating energies
386 requires global communication between all processes which can
387 become a bottleneck at high parallelization.
392 number of steps that elapse between writing energies to energy file,
393 the last energies are always written, should be a multiple of
394 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
395 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
396 energy file, so :ref:`gmx energy` can report exact energy averages
397 and fluctuations also when :mdp:`nstenergy` > 1
399 .. mdp:: nstxout-compressed
402 number of steps that elapse between writing position coordinates
403 using lossy compression (:ref:`xtc` file)
405 .. mdp:: compressed-x-precision
408 precision with which to write to the compressed trajectory file
410 .. mdp:: compressed-x-grps
412 group(s) to write to the compressed trajectory file, by default the
413 whole system is written (if :mdp:`nstxout-compressed` > 0)
417 group(s) for which to write to write short-ranged non-bonded
418 potential energies to the energy file (not supported on GPUs)
424 .. mdp:: cutoff-scheme
426 .. mdp-value:: Verlet
428 Generate a pair list with buffering. The buffer size is
429 automatically set based on :mdp:`verlet-buffer-tolerance`,
430 unless this is set to -1, in which case :mdp:`rlist` will be
431 used. This option has an explicit, exact cut-off at :mdp:`rvdw`
432 equal to :mdp:`rcoulomb`, unless PME or Ewald is used, in which
433 case :mdp:`rcoulomb` > :mdp:`rvdw` is allowed. Currently only
434 cut-off, reaction-field, PME or Ewald electrostatics and plain
435 LJ are supported. Some :ref:`gmx mdrun` functionality is not yet
436 supported with the :mdp-value:`cutoff-scheme=Verlet` scheme, but :ref:`gmx grompp`
437 checks for this. Native GPU acceleration is only supported with
438 :mdp-value:`cutoff-scheme=Verlet`. With GPU-accelerated PME or with separate PME
439 ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
440 balance by scaling :mdp:`rcoulomb` and the grid spacing. This
441 can be turned off with ``mdrun -notunepme``. :mdp-value:`cutoff-scheme=Verlet` is
442 faster than :mdp-value:`cutoff-scheme=group` when there is no water, or if
443 :mdp-value:`cutoff-scheme=group` would use a pair-list buffer to conserve energy.
447 Generate a pair list for groups of atoms. These groups
448 correspond to the charge groups in the topology. This was the
449 only cut-off treatment scheme before version 4.6, and is
450 **deprecated since 5.1**. There is no explicit buffering of
451 the pair list. This enables efficient force calculations for
452 water, but energy is only conserved when a buffer is explicitly
461 Frequency to update the neighbor list. When this is 0, the
462 neighbor list is made only once. With energy minimization the
463 pair list will be updated for every energy evaluation when
464 :mdp:`nstlist` is greater than 0. With :mdp-value:`cutoff-scheme=Verlet` and
465 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
466 a minimum value and :ref:`gmx mdrun` might increase it, unless
467 it is set to 1. With parallel simulations and/or non-bonded
468 force calculation on the GPU, a value of 20 or 40 often gives
469 the best performance. With :mdp-value:`cutoff-scheme=group` and non-exact
470 cut-off's, :mdp:`nstlist` will affect the accuracy of your
471 simulation and it can not be chosen freely.
475 The neighbor list is only constructed once and never
476 updated. This is mainly useful for vacuum simulations in which
477 all particles see each other.
487 Make a grid in the box and only check atoms in neighboring grid
488 cells when constructing a new neighbor list every
489 :mdp:`nstlist` steps. In large systems grid search is much
490 faster than simple search.
492 .. mdp-value:: simple
494 Check every atom in the box when constructing a new neighbor
495 list every :mdp:`nstlist` steps (only with :mdp-value:`cutoff-scheme=group`
502 Use periodic boundary conditions in all directions.
506 Use no periodic boundary conditions, ignore the box. To simulate
507 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
508 best performance without cut-offs on a single MPI rank, set
509 :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`.
513 Use periodic boundary conditions in x and y directions
514 only. This works only with :mdp-value:`ns-type=grid` and can be used
515 in combination with walls_. Without walls or with only one wall
516 the system size is infinite in the z direction. Therefore
517 pressure coupling or Ewald summation methods can not be
518 used. These disadvantages do not apply when two walls are used.
520 .. mdp:: periodic-molecules
524 molecules are finite, fast molecular PBC can be used
528 for systems with molecules that couple to themselves through the
529 periodic boundary conditions, this requires a slower PBC
530 algorithm and molecules are not made whole in the output
532 .. mdp:: verlet-buffer-tolerance
534 (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
536 Useful only with the :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`. This sets
537 the maximum allowed error for pair interactions per particle caused
538 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
539 :mdp:`nstlist` and the Verlet buffer size are fixed (for
540 performance reasons), particle pairs not in the pair list can
541 occasionally get within the cut-off distance during
542 :mdp:`nstlist` -1 steps. This causes very small jumps in the
543 energy. In a constant-temperature ensemble, these very small energy
544 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
545 estimate assumes a homogeneous particle distribution, hence the
546 errors might be slightly underestimated for multi-phase
547 systems. (See the `reference manual`_ for details). For longer
548 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
549 overestimated, because the interactions between particles are
550 ignored. Combined with cancellation of errors, the actual drift of
551 the total energy is usually one to two orders of magnitude
552 smaller. Note that the generated buffer size takes into account
553 that the |Gromacs| pair-list setup leads to a reduction in the
554 drift by a factor 10, compared to a simple particle-pair based
555 list. Without dynamics (energy minimization etc.), the buffer is 5%
556 of the cut-off. For NVE simulations the initial temperature is
557 used, unless this is zero, in which case a buffer of 10% is
558 used. For NVE simulations the tolerance usually needs to be lowered
559 to achieve proper energy conservation on the nanosecond time
560 scale. To override the automated buffer setting, use
561 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
566 Cut-off distance for the short-range neighbor list. With the
567 :mdp-value:`cutoff-scheme=Verlet` :mdp:`cutoff-scheme`, this is by default set by the
568 :mdp:`verlet-buffer-tolerance` option and the value of
569 :mdp:`rlist` is ignored.
577 .. mdp-value:: Cut-off
579 Plain cut-off with pair list radius :mdp:`rlist` and
580 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
585 Classical Ewald sum electrostatics. The real-space cut-off
586 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
587 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
588 of wave vectors used in reciprocal space is controlled by
589 :mdp:`fourierspacing`. The relative accuracy of
590 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
592 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
593 large systems. It is included mainly for reference - in most
594 cases PME will perform much better.
598 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
599 space is similar to the Ewald sum, while the reciprocal part is
600 performed with FFTs. Grid dimensions are controlled with
601 :mdp:`fourierspacing` and the interpolation order with
602 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
603 interpolation the electrostatic forces have an accuracy of
604 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
605 this you might try 0.15 nm. When running in parallel the
606 interpolation parallelizes better than the FFT, so try
607 decreasing grid dimensions while increasing interpolation.
609 .. mdp-value:: P3M-AD
611 Particle-Particle Particle-Mesh algorithm with analytical
612 derivative for for long range electrostatic interactions. The
613 method and code is identical to SPME, except that the influence
614 function is optimized for the grid. This gives a slight increase
617 .. mdp-value:: Reaction-Field
619 Reaction field electrostatics with Coulomb cut-off
620 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
621 dielectric constant beyond the cut-off is
622 :mdp:`epsilon-rf`. The dielectric constant can be set to
623 infinity by setting :mdp:`epsilon-rf` =0.
625 .. mdp-value:: Generalized-Reaction-Field
627 Generalized reaction field with Coulomb cut-off
628 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rcoulomb`. The
629 dielectric constant beyond the cut-off is
630 :mdp:`epsilon-rf`. The ionic strength is computed from the
631 number of charged (*i.e.* with non zero charge) charge
632 groups. The temperature for the GRF potential is set with
635 .. mdp-value:: Reaction-Field-zero
637 In |Gromacs|, normal reaction-field electrostatics with
638 :mdp-value:`cutoff-scheme=group` leads to bad energy
639 conservation. :mdp-value:`coulombtype=Reaction-Field-zero` solves this by making
640 the potential zero beyond the cut-off. It can only be used with
641 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
642 only for that value the force vanishes at the
643 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
644 :mdp:`rcoulomb` to accommodate the size of charge groups
645 and diffusion between neighbor list updates. This, and the fact
646 that table lookups are used instead of analytical functions make
647 reaction-field-zero computationally more expensive than
648 normal reaction-field.
652 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
653 might want to use :mdp-value:`coulombtype=Reaction-Field-zero` instead, which has
654 a similar potential shape, but has a physical interpretation and
655 has better energies due to the exclusion correction terms.
657 .. mdp-value:: Encad-Shift
659 The Coulomb potential is decreased over the whole range, using
660 the definition from the Encad simulation package.
662 .. mdp-value:: Switch
664 Analogous to :mdp-value:`vdwtype=Switch` for
665 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
666 serious artifacts, advice: use :mdp-value:`coulombtype=Reaction-Field-zero`
671 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
672 with user-defined potential functions for repulsion, dispersion
673 and Coulomb. When pair interactions are present, :ref:`gmx
674 mdrun` also expects to find a file ``tablep.xvg`` for the pair
675 interactions. When the same interactions should be used for
676 non-bonded and pair interactions the user can specify the same
677 file name for both table files. These files should contain 7
678 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
679 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
680 function, ``g(x)`` the dispersion function and ``h(x)`` the
681 repulsion function. When :mdp:`vdwtype` is not set to User the
682 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
683 the non-bonded interactions ``x`` values should run from 0 to
684 the largest cut-off distance + :mdp:`table-extension` and
685 should be uniformly spaced. For the pair interactions the table
686 length in the file will be used. The optimal spacing, which is
687 used for non-user tables, is ``0.002 nm`` when you run in mixed
688 precision or ``0.0005 nm`` when you run in double precision. The
689 function value at ``x=0`` is not important. More information is
690 in the printed manual.
692 .. mdp-value:: PME-Switch
694 A combination of PME and a switch function for the direct-space
695 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
696 :mdp:`rlist`. This is mainly useful constant energy simulations
697 (note that using PME with :mdp-value:`cutoff-scheme=Verlet`
698 will be more efficient).
700 .. mdp-value:: PME-User
702 A combination of PME and user tables (see
703 above). :mdp:`rcoulomb` is allowed to be smaller than
704 :mdp:`rlist`. The PME mesh contribution is subtracted from the
705 user table by :ref:`gmx mdrun`. Because of this subtraction the
706 user tables should contain about 10 decimal places.
708 .. mdp-value:: PME-User-Switch
710 A combination of PME-User and a switching function (see
711 above). The switching function is applied to final
712 particle-particle interaction, *i.e.* both to the user supplied
713 function and the PME Mesh correction part.
715 .. mdp:: coulomb-modifier
717 .. mdp-value:: Potential-shift-Verlet
719 Selects Potential-shift with the Verlet cutoff-scheme, as it is
720 (nearly) free; selects None with the group cutoff-scheme.
722 .. mdp-value:: Potential-shift
724 Shift the Coulomb potential by a constant such that it is zero
725 at the cut-off. This makes the potential the integral of the
726 force. Note that this does not affect the forces or the
731 Use an unmodified Coulomb potential. With the group scheme this
732 means no exact cut-off is used, energies and forces are
733 calculated for all pairs in the pair list.
735 .. mdp:: rcoulomb-switch
738 where to start switching the Coulomb potential, only relevant
739 when force or potential switching is used
744 The distance for the Coulomb cut-off. Note that with PME this value
745 can be increased by the PME tuning in :ref:`gmx mdrun` along with
746 the PME grid spacing.
751 The relative dielectric constant. A value of 0 means infinity.
756 The relative dielectric constant of the reaction field. This
757 is only used with reaction-field electrostatics. A value of 0
766 .. mdp-value:: Cut-off
768 Plain cut-off with pair list radius :mdp:`rlist` and VdW
769 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
773 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
774 grid dimensions are controlled with :mdp:`fourierspacing` in
775 the same way as for electrostatics, and the interpolation order
776 is controlled with :mdp:`pme-order`. The relative accuracy of
777 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
778 and the specific combination rules that are to be used by the
779 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
783 This functionality is deprecated and replaced by using
784 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
785 The LJ (not Buckingham) potential is decreased over the whole range and
786 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
787 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
788 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
789 size of charge groups and diffusion between neighbor list
792 .. mdp-value:: Switch
794 This functionality is deprecated and replaced by using
795 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
796 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
797 which it is switched off to reach zero at :mdp:`rvdw`. Both the
798 potential and force functions are continuously smooth, but be
799 aware that all switch functions will give rise to a bulge
800 (increase) in the force (since we are switching the
801 potential). The neighbor search cut-off :mdp:`rlist` should be
802 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate the
803 size of charge groups and diffusion between neighbor list
806 .. mdp-value:: Encad-Shift
808 The LJ (not Buckingham) potential is decreased over the whole
809 range, using the definition from the Encad simulation package.
813 See user for :mdp:`coulombtype`. The function value at zero is
814 not important. When you want to use LJ correction, make sure
815 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
816 function. When :mdp:`coulombtype` is not set to User the values
817 for the ``f`` and ``-f'`` columns are ignored.
819 .. mdp:: vdw-modifier
821 .. mdp-value:: Potential-shift-Verlet
823 Selects Potential-shift with the Verlet cutoff-scheme, as it is
824 (nearly) free; selects None with the group cutoff-scheme.
826 .. mdp-value:: Potential-shift
828 Shift the Van der Waals potential by a constant such that it is
829 zero at the cut-off. This makes the potential the integral of
830 the force. Note that this does not affect the forces or the
835 Use an unmodified Van der Waals potential. With the group scheme
836 this means no exact cut-off is used, energies and forces are
837 calculated for all pairs in the pair list.
839 .. mdp-value:: Force-switch
841 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
842 and :mdp:`rvdw`. This shifts the potential shift over the whole
843 range and switches it to zero at the cut-off. Note that this is
844 more expensive to calculate than a plain cut-off and it is not
845 required for energy conservation, since Potential-shift
846 conserves energy just as well.
848 .. mdp-value:: Potential-switch
850 Smoothly switches the potential to zero between
851 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
852 articifically large forces in the switching region and is much
853 more expensive to calculate. This option should only be used if
854 the force field you are using requires this.
859 where to start switching the LJ force and possibly the potential,
860 only relevant when force or potential switching is used
865 distance for the LJ or Buckingham cut-off
871 don't apply any correction
873 .. mdp-value:: EnerPres
875 apply long range dispersion corrections for Energy and Pressure
879 apply long range dispersion corrections for Energy only
885 .. mdp:: table-extension
888 Extension of the non-bonded potential lookup tables beyond the
889 largest cut-off distance. The value should be large enough to
890 account for charge group sizes and the diffusion between
891 neighbor-list updates. Without user defined potential the same
892 table length is used for the lookup tables for the 1-4
893 interactions, which are always tabulated irrespective of the use of
894 tables for the non-bonded interactions. The value of
895 :mdp:`table-extension` in no way affects the values of
896 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
898 .. mdp:: energygrp-table
900 When user tables are used for electrostatics and/or VdW, here one
901 can give pairs of energy groups for which seperate user tables
902 should be used. The two energy groups will be appended to the table
903 file name, in order of their definition in :mdp:`energygrps`,
904 seperated by underscores. For example, if ``energygrps = Na Cl
905 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
906 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
907 normal ``table.xvg`` which will be used for all other energy group
914 .. mdp:: fourierspacing
917 For ordinary Ewald, the ratio of the box dimensions and the spacing
918 determines a lower bound for the number of wave vectors to use in
919 each (signed) direction. For PME and P3M, that ratio determines a
920 lower bound for the number of Fourier-space grid points that will
921 be used along that axis. In all cases, the number for each
922 direction can be overridden by entering a non-zero value for that
923 :mdp:`fourier-nx` direction. For optimizing the relative load of
924 the particle-particle interactions and the mesh part of PME, it is
925 useful to know that the accuracy of the electrostatics remains
926 nearly constant when the Coulomb cut-off and the PME grid spacing
927 are scaled by the same factor. Note that this spacing can be scaled
928 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
935 Highest magnitude of wave vectors in reciprocal space when using Ewald.
936 Grid size when using PME or P3M. These values override
937 :mdp:`fourierspacing` per direction. The best choice is powers of
938 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
939 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
945 Interpolation order for PME. 4 equals cubic interpolation. You
946 might try 6/8/10 when running in parallel and simultaneously
947 decrease grid dimension.
952 The relative strength of the Ewald-shifted direct potential at
953 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
954 will give a more accurate direct sum, but then you need more wave
955 vectors for the reciprocal sum.
957 .. mdp:: ewald-rtol-lj
960 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
961 to control the relative strength of the dispersion potential at
962 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
963 electrostatic potential.
965 .. mdp:: lj-pme-comb-rule
968 The combination rules used to combine VdW-parameters in the
969 reciprocal part of LJ-PME. Geometric rules are much faster than
970 Lorentz-Berthelot and usually the recommended choice, even when the
971 rest of the force field uses the Lorentz-Berthelot rules.
973 .. mdp-value:: Geometric
975 Apply geometric combination rules
977 .. mdp-value:: Lorentz-Berthelot
979 Apply Lorentz-Berthelot combination rules
981 .. mdp:: ewald-geometry
985 The Ewald sum is performed in all three dimensions.
989 The reciprocal sum is still performed in 3D, but a force and
990 potential correction applied in the `z` dimension to produce a
991 pseudo-2D summation. If your system has a slab geometry in the
992 `x-y` plane you can try to increase the `z`-dimension of the box
993 (a box height of 3 times the slab height is usually ok) and use
996 .. mdp:: epsilon-surface
999 This controls the dipole correction to the Ewald summation in
1000 3D. The default value of zero means it is turned off. Turn it on by
1001 setting it to the value of the relative permittivity of the
1002 imaginary surface around your infinite system. Be careful - you
1003 shouldn't use this if you have free mobile charges in your
1004 system. This value does not affect the slab 3DC variant of the long
1008 Temperature coupling
1009 ^^^^^^^^^^^^^^^^^^^^
1015 No temperature coupling.
1017 .. mdp-value:: berendsen
1019 Temperature coupling with a Berendsen thermostat to a bath with
1020 temperature :mdp:`ref-t`, with time constant
1021 :mdp:`tau-t`. Several groups can be coupled separately, these
1022 are specified in the :mdp:`tc-grps` field separated by spaces.
1024 .. mdp-value:: nose-hoover
1026 Temperature coupling using a Nose-Hoover extended ensemble. The
1027 reference temperature and coupling groups are selected as above,
1028 but in this case :mdp:`tau-t` controls the period of the
1029 temperature fluctuations at equilibrium, which is slightly
1030 different from a relaxation time. For NVT simulations the
1031 conserved energy quantity is written to the energy and log files.
1033 .. mdp-value:: andersen
1035 Temperature coupling by randomizing a fraction of the particle velocities
1036 at each timestep. Reference temperature and coupling groups are
1037 selected as above. :mdp:`tau-t` is the average time between
1038 randomization of each molecule. Inhibits particle dynamics
1039 somewhat, but little or no ergodicity issues. Currently only
1040 implemented with velocity Verlet, and not implemented with
1043 .. mdp-value:: andersen-massive
1045 Temperature coupling by randomizing velocities of all particles at
1046 infrequent timesteps. Reference temperature and coupling groups are
1047 selected as above. :mdp:`tau-t` is the time between
1048 randomization of all molecules. Inhibits particle dynamics
1049 somewhat, but little or no ergodicity issues. Currently only
1050 implemented with velocity Verlet.
1052 .. mdp-value:: v-rescale
1054 Temperature coupling using velocity rescaling with a stochastic
1055 term (JCP 126, 014101). This thermostat is similar to Berendsen
1056 coupling, with the same scaling using :mdp:`tau-t`, but the
1057 stochastic term ensures that a proper canonical ensemble is
1058 generated. The random seed is set with :mdp:`ld-seed`. This
1059 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1060 simulations the conserved energy quantity is written to the
1061 energy and log file.
1066 The frequency for coupling the temperature. The default value of -1
1067 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1068 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1069 Verlet integrators :mdp:`nsttcouple` is set to 1.
1071 .. mdp:: nh-chain-length
1074 The number of chained Nose-Hoover thermostats for velocity Verlet
1075 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1076 only supports 1. Data for the NH chain variables is not printed
1077 to the :ref:`edr` file by default, but can be turned on with the
1078 :mdp:`print-nose-hoover-chains` option.
1080 .. mdp:: print-nose-hoover-chain-variables
1084 Do not store Nose-Hoover chain variables in the energy file.
1088 Store all positions and velocities of the Nose-Hoover chain
1093 groups to couple to separate temperature baths
1098 time constant for coupling (one for each group in
1099 :mdp:`tc-grps`), -1 means no temperature coupling
1104 reference temperature for coupling (one for each group in
1115 No pressure coupling. This means a fixed box size.
1117 .. mdp-value:: Berendsen
1119 Exponential relaxation pressure coupling with time constant
1120 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1121 argued that this does not yield a correct thermodynamic
1122 ensemble, but it is the most efficient way to scale a box at the
1125 .. mdp-value:: Parrinello-Rahman
1127 Extended-ensemble pressure coupling where the box vectors are
1128 subject to an equation of motion. The equation of motion for the
1129 atoms is coupled to this. No instantaneous scaling takes
1130 place. As for Nose-Hoover temperature coupling the time constant
1131 :mdp:`tau-p` is the period of pressure fluctuations at
1132 equilibrium. This is probably a better method when you want to
1133 apply pressure scaling during data collection, but beware that
1134 you can get very large oscillations if you are starting from a
1135 different pressure. For simulations where the exact fluctations
1136 of the NPT ensemble are important, or if the pressure coupling
1137 time is very short it may not be appropriate, as the previous
1138 time step pressure is used in some steps of the |Gromacs|
1139 implementation for the current time step pressure.
1143 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1144 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1145 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1146 time constant :mdp:`tau-p` is the period of pressure
1147 fluctuations at equilibrium. This is probably a better method
1148 when you want to apply pressure scaling during data collection,
1149 but beware that you can get very large oscillations if you are
1150 starting from a different pressure. Currently (as of version
1151 5.1), it only supports isotropic scaling, and only works without
1156 Specifies the kind of isotropy of the pressure coupling used. Each
1157 kind takes one or more values for :mdp:`compressibility` and
1158 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1160 .. mdp-value:: isotropic
1162 Isotropic pressure coupling with time constant
1163 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1164 :mdp:`ref-p` is required.
1166 .. mdp-value:: semiisotropic
1168 Pressure coupling which is isotropic in the ``x`` and ``y``
1169 direction, but different in the ``z`` direction. This can be
1170 useful for membrane simulations. Two values each for
1171 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1172 ``x/y`` and ``z`` directions respectively.
1174 .. mdp-value:: anisotropic
1176 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1177 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1178 respectively. When the off-diagonal compressibilities are set to
1179 zero, a rectangular box will stay rectangular. Beware that
1180 anisotropic scaling can lead to extreme deformation of the
1183 .. mdp-value:: surface-tension
1185 Surface tension coupling for surfaces parallel to the
1186 xy-plane. Uses normal pressure coupling for the `z`-direction,
1187 while the surface tension is coupled to the `x/y` dimensions of
1188 the box. The first :mdp:`ref-p` value is the reference surface
1189 tension times the number of surfaces ``bar nm``, the second
1190 value is the reference `z`-pressure ``bar``. The two
1191 :mdp:`compressibility` values are the compressibility in the
1192 `x/y` and `z` direction respectively. The value for the
1193 `z`-compressibility should be reasonably accurate since it
1194 influences the convergence of the surface-tension, it can also
1195 be set to zero to have a box with constant height.
1200 The frequency for coupling the pressure. The default value of -1
1201 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1202 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1203 Verlet integrators :mdp:`nstpcouple` is set to 1.
1208 The time constant for pressure coupling (one value for all
1211 .. mdp:: compressibility
1214 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1215 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1216 required values is implied by :mdp:`pcoupltype`.
1221 The reference pressure for coupling. The number of required values
1222 is implied by :mdp:`pcoupltype`.
1224 .. mdp:: refcoord-scaling
1228 The reference coordinates for position restraints are not
1229 modified. Note that with this option the virial and pressure
1230 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1235 The reference coordinates are scaled with the scaling matrix of
1236 the pressure coupling.
1240 Scale the center of mass of the reference coordinates with the
1241 scaling matrix of the pressure coupling. The vectors of each
1242 reference coordinate to the center of mass are not scaled. Only
1243 one COM is used, even when there are multiple molecules with
1244 position restraints. For calculating the COM of the reference
1245 coordinates in the starting configuration, periodic boundary
1246 conditions are not taken into account. Note that with this option
1247 the virial and pressure might be ill defined, see
1248 :ref:`here <reference-manual-position-restraints>` for more details.
1254 Simulated annealing is controlled separately for each temperature
1255 group in |Gromacs|. The reference temperature is a piecewise linear
1256 function, but you can use an arbitrary number of points for each
1257 group, and choose either a single sequence or a periodic behaviour for
1258 each group. The actual annealing is performed by dynamically changing
1259 the reference temperature used in the thermostat algorithm selected,
1260 so remember that the system will usually not instantaneously reach the
1261 reference temperature!
1265 Type of annealing for each temperature group
1269 No simulated annealing - just couple to reference temperature value.
1271 .. mdp-value:: single
1273 A single sequence of annealing points. If your simulation is
1274 longer than the time of the last point, the temperature will be
1275 coupled to this constant value after the annealing sequence has
1276 reached the last time point.
1278 .. mdp-value:: periodic
1280 The annealing will start over at the first reference point once
1281 the last reference time is reached. This is repeated until the
1284 .. mdp:: annealing-npoints
1286 A list with the number of annealing reference/control points used
1287 for each temperature group. Use 0 for groups that are not
1288 annealed. The number of entries should equal the number of
1291 .. mdp:: annealing-time
1293 List of times at the annealing reference/control points for each
1294 group. If you are using periodic annealing, the times will be used
1295 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1296 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1297 etc. The number of entries should equal the sum of the numbers
1298 given in :mdp:`annealing-npoints`.
1300 .. mdp:: annealing-temp
1302 List of temperatures at the annealing reference/control points for
1303 each group. The number of entries should equal the sum of the
1304 numbers given in :mdp:`annealing-npoints`.
1306 Confused? OK, let's use an example. Assume you have two temperature
1307 groups, set the group selections to ``annealing = single periodic``,
1308 the number of points of each group to ``annealing-npoints = 3 4``, the
1309 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1310 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1311 will be coupled to 298K at 0ps, but the reference temperature will
1312 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1313 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1314 second group is coupled to 298K at 0ps, it increases linearly to 320K
1315 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1316 decreases to 298K, and then it starts over with the same pattern
1317 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1318 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1328 Do not generate velocities. The velocities are set to zero
1329 when there are no velocities in the input structure file.
1333 Generate velocities in :ref:`gmx grompp` according to a
1334 Maxwell distribution at temperature :mdp:`gen-temp`, with
1335 random seed :mdp:`gen-seed`. This is only meaningful with
1336 :mdp-value:`integrator=md`.
1341 temperature for Maxwell distribution
1346 used to initialize random generator for random velocities,
1347 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1354 .. mdp:: constraints
1356 Controls which bonds in the topology will be converted to rigid
1357 holonomic constraints. Note that typical rigid water models do not
1358 have bonds, but rather a specialized ``[settles]`` directive, so
1359 are not affected by this keyword.
1363 No bonds converted to constraints.
1365 .. mdp-value:: h-bonds
1367 Convert the bonds with H-atoms to constraints.
1369 .. mdp-value:: all-bonds
1371 Convert all bonds to constraints.
1373 .. mdp-value:: h-angles
1375 Convert all bonds to constraints and convert the angles that
1376 involve H-atoms to bond-constraints.
1378 .. mdp-value:: all-angles
1380 Convert all bonds to constraints and all angles to bond-constraints.
1382 .. mdp:: constraint-algorithm
1384 Chooses which solver satisfies any non-SETTLE holonomic
1387 .. mdp-value:: LINCS
1389 LINear Constraint Solver. With domain decomposition the parallel
1390 version P-LINCS is used. The accuracy in set with
1391 :mdp:`lincs-order`, which sets the number of matrices in the
1392 expansion for the matrix inversion. After the matrix inversion
1393 correction the algorithm does an iterative correction to
1394 compensate for lengthening due to rotation. The number of such
1395 iterations can be controlled with :mdp:`lincs-iter`. The root
1396 mean square relative constraint deviation is printed to the log
1397 file every :mdp:`nstlog` steps. If a bond rotates more than
1398 :mdp:`lincs-warnangle` in one step, a warning will be printed
1399 both to the log file and to ``stderr``. LINCS should not be used
1400 with coupled angle constraints.
1402 .. mdp-value:: SHAKE
1404 SHAKE is slightly slower and less stable than LINCS, but does
1405 work with angle constraints. The relative tolerance is set with
1406 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1407 does not support constraints between atoms on different nodes,
1408 thus it can not be used with domain decompositon when inter
1409 charge-group constraints are present. SHAKE can not be used with
1410 energy minimization.
1412 .. mdp:: continuation
1414 This option was formerly known as ``unconstrained-start``.
1418 apply constraints to the start configuration and reset shells
1422 do not apply constraints to the start configuration and do not
1423 reset shells, useful for exact coninuation and reruns
1428 relative tolerance for SHAKE
1430 .. mdp:: lincs-order
1433 Highest order in the expansion of the constraint coupling
1434 matrix. When constraints form triangles, an additional expansion of
1435 the same order is applied on top of the normal expansion only for
1436 the couplings within such triangles. For "normal" MD simulations an
1437 order of 4 usually suffices, 6 is needed for large time-steps with
1438 virtual sites or BD. For accurate energy minimization an order of 8
1439 or more might be required. With domain decomposition, the cell size
1440 is limited by the distance spanned by :mdp:`lincs-order` +1
1441 constraints. When one wants to scale further than this limit, one
1442 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1443 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1444 )* :mdp:`lincs-order` remains constant.
1449 Number of iterations to correct for rotational lengthening in
1450 LINCS. For normal runs a single step is sufficient, but for NVE
1451 runs where you want to conserve energy accurately or for accurate
1452 energy minimization you might want to increase it to 2.
1454 .. mdp:: lincs-warnangle
1457 maximum angle that a bond can rotate before LINCS will complain
1463 bonds are represented by a harmonic potential
1467 bonds are represented by a Morse potential
1470 Energy group exclusions
1471 ^^^^^^^^^^^^^^^^^^^^^^^
1473 .. mdp:: energygrp-excl
1475 Pairs of energy groups for which all non-bonded interactions are
1476 excluded. An example: if you have two energy groups ``Protein`` and
1477 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1478 would give only the non-bonded interactions between the protein and
1479 the solvent. This is especially useful for speeding up energy
1480 calculations with ``mdrun -rerun`` and for excluding interactions
1481 within frozen groups.
1490 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1491 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1492 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1493 used (it is usually best to use semiisotropic pressure coupling
1494 with the ``x/y`` compressibility set to 0, as otherwise the surface
1495 area will change). Walls interact wit the rest of the system
1496 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1497 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1498 monitor the interaction of energy groups with each wall. The center
1499 of mass motion removal will be turned off in the ``z``-direction.
1501 .. mdp:: wall-atomtype
1503 the atom type name in the force field for each wall. By (for
1504 example) defining a special wall atom type in the topology with its
1505 own combination rules, this allows for independent tuning of the
1506 interaction of each atomtype with the walls.
1512 LJ integrated over the volume behind the wall: 9-3 potential
1516 LJ integrated over the wall surface: 10-4 potential
1520 direct LJ potential with the ``z`` distance from the wall
1524 user defined potentials indexed with the ``z`` distance from the
1525 wall, the tables are read analogously to the
1526 :mdp:`energygrp-table` option, where the first name is for a
1527 "normal" energy group and the second name is ``wall0`` or
1528 ``wall1``, only the dispersion and repulsion columns are used
1530 .. mdp:: wall-r-linpot
1533 Below this distance from the wall the potential is continued
1534 linearly and thus the force is constant. Setting this option to a
1535 postive value is especially useful for equilibration when some
1536 atoms are beyond a wall. When the value is <=0 (<0 for
1537 :mdp:`wall-type` =table), a fatal error is generated when atoms
1540 .. mdp:: wall-density
1542 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1543 the number density of the atoms for each wall for wall types 9-3
1546 .. mdp:: wall-ewald-zfac
1549 The scaling factor for the third box vector for Ewald summation
1550 only, the minimum is 2. Ewald summation can only be used with
1551 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1552 ``=3dc``. The empty layer in the box serves to decrease the
1553 unphysical Coulomb interaction between periodic images.
1559 Note that where pulling coordinates are applicable, there can be more
1560 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1561 variables will exist accordingly. Documentation references to things
1562 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1563 applicable pulling coordinate, eg. the second pull coordinate is described by
1564 pull-coord2-vec, pull-coord2-k, and so on.
1570 No center of mass pulling. All the following pull options will
1571 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1576 Center of mass pulling will be applied on 1 or more groups using
1577 1 or more pull coordinates.
1579 .. mdp:: pull-cylinder-r
1582 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1584 .. mdp:: pull-constr-tol
1587 the relative constraint tolerance for constraint pulling
1589 .. mdp:: pull-print-com
1593 do not print the COM for any group
1597 print the COM of all groups for all pull coordinates
1599 .. mdp:: pull-print-ref-value
1603 do not print the reference value for each pull coordinate
1607 print the reference value for each pull coordinate
1609 .. mdp:: pull-print-components
1613 only print the distance for each pull coordinate
1617 print the distance and Cartesian components selected in
1618 :mdp:`pull-coord1-dim`
1620 .. mdp:: pull-nstxout
1623 frequency for writing out the COMs of all the pull group (0 is
1626 .. mdp:: pull-nstfout
1629 frequency for writing out the force of all the pulled group
1632 .. mdp:: pull-pbc-ref-prev-step-com
1636 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1637 treatment of periodic boundary conditions.
1641 Use the COM of the previous step as reference for the treatment
1642 of periodic boundary conditions. The reference is initialized
1643 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1644 be located centrally in the group. Using the COM from the
1645 previous step can be useful if one or more pull groups are large.
1647 .. mdp:: pull-xout-average
1651 Write the instantaneous coordinates for all the pulled groups.
1655 Write the average coordinates (since last output) for all the
1656 pulled groups. N.b., some analysis tools might expect instantaneous
1659 .. mdp:: pull-fout-average
1663 Write the instantaneous force for all the pulled groups.
1667 Write the average force (since last output) for all the
1668 pulled groups. N.b., some analysis tools might expect instantaneous
1671 .. mdp:: pull-ngroups
1674 The number of pull groups, not including the absolute reference
1675 group, when used. Pull groups can be reused in multiple pull
1676 coordinates. Below only the pull options for group 1 are given,
1677 further groups simply increase the group index number.
1679 .. mdp:: pull-ncoords
1682 The number of pull coordinates. Below only the pull options for
1683 coordinate 1 are given, further coordinates simply increase the
1684 coordinate index number.
1686 .. mdp:: pull-group1-name
1688 The name of the pull group, is looked up in the index file or in
1689 the default groups to obtain the atoms involved.
1691 .. mdp:: pull-group1-weights
1693 Optional relative weights which are multiplied with the masses of
1694 the atoms to give the total weight for the COM. The number should
1695 be 0, meaning all 1, or the number of atoms in the pull group.
1697 .. mdp:: pull-group1-pbcatom
1700 The reference atom for the treatment of periodic boundary
1701 conditions inside the group (this has no effect on the treatment of
1702 the pbc between groups). This option is only important when the
1703 diameter of the pull group is larger than half the shortest box
1704 vector. For determining the COM, all atoms in the group are put at
1705 their periodic image which is closest to
1706 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1707 atom (number wise) is used, which is only safe for small groups.
1708 :ref:`gmx grompp` checks that the maximum distance from the reference
1709 atom (specifically chosen, or not) to the other atoms in the group
1710 is not too large. This parameter is not used with
1711 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1712 weighting, which is useful for a group of molecules in a periodic
1713 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1716 .. mdp:: pull-coord1-type
1718 .. mdp-value:: umbrella
1720 Center of mass pulling using an umbrella potential between the
1721 reference group and one or more groups.
1723 .. mdp-value:: constraint
1725 Center of mass pulling using a constraint between the reference
1726 group and one or more groups. The setup is identical to the
1727 option umbrella, except for the fact that a rigid constraint is
1728 applied instead of a harmonic potential.
1730 .. mdp-value:: constant-force
1732 Center of mass pulling using a linear potential and therefore a
1733 constant force. For this option there is no reference position
1734 and therefore the parameters :mdp:`pull-coord1-init` and
1735 :mdp:`pull-coord1-rate` are not used.
1737 .. mdp-value:: flat-bottom
1739 At distances above :mdp:`pull-coord1-init` a harmonic potential
1740 is applied, otherwise no potential is applied.
1742 .. mdp-value:: flat-bottom-high
1744 At distances below :mdp:`pull-coord1-init` a harmonic potential
1745 is applied, otherwise no potential is applied.
1747 .. mdp-value:: external-potential
1749 An external potential that needs to be provided by another
1752 .. mdp:: pull-coord1-potential-provider
1754 The name of the external module that provides the potential for
1755 the case where :mdp:`pull-coord1-type` is external-potential.
1757 .. mdp:: pull-coord1-geometry
1759 .. mdp-value:: distance
1761 Pull along the vector connecting the two groups. Components can
1762 be selected with :mdp:`pull-coord1-dim`.
1764 .. mdp-value:: direction
1766 Pull in the direction of :mdp:`pull-coord1-vec`.
1768 .. mdp-value:: direction-periodic
1770 As :mdp-value:`pull-coord1-geometry=direction`, but does not apply
1771 periodic box vector corrections to keep the distance within half
1772 the box length. This is (only) useful for pushing groups apart
1773 by more than half the box length by continuously changing the reference
1774 location using a pull rate. With this geometry the box should not be
1775 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1776 the pull force is not added to the virial.
1778 .. mdp-value:: direction-relative
1780 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1781 that points from the COM of a third to the COM of a fourth pull
1782 group. This means that 4 groups need to be supplied in
1783 :mdp:`pull-coord1-groups`. Note that the pull force will give
1784 rise to a torque on the pull vector, which is turn leads to
1785 forces perpendicular to the pull vector on the two groups
1786 defining the vector. If you want a pull group to move between
1787 the two groups defining the vector, simply use the union of
1788 these two groups as the reference group.
1790 .. mdp-value:: cylinder
1792 Designed for pulling with respect to a layer where the reference
1793 COM is given by a local cylindrical part of the reference group.
1794 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1795 the first of the two groups in :mdp:`pull-coord1-groups` a
1796 cylinder is selected around the axis going through the COM of
1797 the second group with direction :mdp:`pull-coord1-vec` with
1798 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1799 continously to zero as the radial distance goes from 0 to
1800 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1801 dependence gives rise to radial forces on both pull groups.
1802 Note that the radius should be smaller than half the box size.
1803 For tilted cylinders they should be even smaller than half the
1804 box size since the distance of an atom in the reference group
1805 from the COM of the pull group has both a radial and an axial
1806 component. This geometry is not supported with constraint
1809 .. mdp-value:: angle
1811 Pull along an angle defined by four groups. The angle is
1812 defined as the angle between two vectors: the vector connecting
1813 the COM of the first group to the COM of the second group and
1814 the vector connecting the COM of the third group to the COM of
1817 .. mdp-value:: angle-axis
1819 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1820 Thus, only the two groups that define the first vector need to be given.
1822 .. mdp-value:: dihedral
1824 Pull along a dihedral angle defined by six groups. These pairwise
1825 define three vectors: the vector connecting the COM of group 1
1826 to the COM of group 2, the COM of group 3 to the COM of group 4,
1827 and the COM of group 5 to the COM group 6. The dihedral angle is
1828 then defined as the angle between two planes: the plane spanned by the
1829 the two first vectors and the plane spanned the two last vectors.
1832 .. mdp:: pull-coord1-groups
1834 The group indices on which this pull coordinate will operate.
1835 The number of group indices required is geometry dependent.
1836 The first index can be 0, in which case an
1837 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1838 absolute reference the system is no longer translation invariant
1839 and one should think about what to do with the center of mass
1842 .. mdp:: pull-coord1-dim
1845 Selects the dimensions that this pull coordinate acts on and that
1846 are printed to the output files when
1847 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1848 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1849 components set to Y contribute to the distance. Thus setting this
1850 to Y Y N results in a distance in the x/y plane. With other
1851 geometries all dimensions with non-zero entries in
1852 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1853 dimensions only affect the output.
1855 .. mdp:: pull-coord1-origin
1858 The pull reference position for use with an absolute reference.
1860 .. mdp:: pull-coord1-vec
1863 The pull direction. :ref:`gmx grompp` normalizes the vector.
1865 .. mdp:: pull-coord1-start
1869 do not modify :mdp:`pull-coord1-init`
1873 add the COM distance of the starting conformation to
1874 :mdp:`pull-coord1-init`
1876 .. mdp:: pull-coord1-init
1879 The reference distance or reference angle at t=0.
1881 .. mdp:: pull-coord1-rate
1883 (0) [nm/ps] or [deg/ps]
1884 The rate of change of the reference position or reference angle.
1886 .. mdp:: pull-coord1-k
1888 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1889 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1890 The force constant. For umbrella pulling this is the harmonic force
1891 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1892 for angles). For constant force pulling this is the
1893 force constant of the linear potential, and thus the negative (!)
1894 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1895 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1896 Note that for angles the force constant is expressed in terms of radians
1897 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1899 .. mdp:: pull-coord1-kB
1901 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1902 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1903 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1904 :mdp:`free-energy` is turned on. The force constant is then (1 -
1905 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1907 AWH adaptive biasing
1908 ^^^^^^^^^^^^^^^^^^^^
1918 Adaptively bias a reaction coordinate using the AWH method and estimate
1919 the corresponding PMF. The PMF and other AWH data are written to energy
1920 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1921 the ``gmx awh`` tool. The AWH coordinate can be
1922 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1923 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1924 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1925 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1927 .. mdp:: awh-potential
1929 .. mdp-value:: convolved
1931 The applied biasing potential is the convolution of the bias function and a
1932 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1933 in a smooth potential function and force. The resolution of the potential is set
1934 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1936 .. mdp-value:: umbrella
1938 The potential bias is applied by controlling the position of an harmonic potential
1939 using Monte-Carlo sampling. The force constant is set with
1940 :mdp:`awh1-dim1-force-constant`. The umbrella location
1941 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1942 There are no advantages to using an umbrella.
1943 This option is mainly for comparison and testing purposes.
1945 .. mdp:: awh-share-multisim
1949 AWH will not share biases across simulations started with
1950 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1954 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1955 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1956 with the biases with the same :mdp:`awh1-share-group` value.
1957 The simulations should have the same AWH settings for sharing to make sense.
1958 :ref:`gmx mdrun` will check whether the simulations are technically
1959 compatible for sharing, but the user should check that bias sharing
1960 physically makes sense.
1964 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1965 where -1 indicates to generate a seed. Only used with
1966 :mdp-value:`awh-potential=umbrella`.
1971 Number of steps between printing AWH data to the energy file, should be
1972 a multiple of :mdp:`nstenergy`.
1974 .. mdp:: awh-nstsample
1977 Number of steps between sampling of the coordinate value. This sampling
1978 is the basis for updating the bias and estimating the PMF and other AWH observables.
1980 .. mdp:: awh-nsamples-update
1983 The number of coordinate samples used for each AWH update.
1984 The update interval in steps is :mdp:`awh-nstsample` times this value.
1989 The number of biases, each acting on its own coordinate.
1990 The following options should be specified
1991 for each bias although below only the options for bias number 1 is shown. Options for
1992 other bias indices are obtained by replacing '1' by the bias index.
1994 .. mdp:: awh1-error-init
1996 (10.0) [kJ mol\ :sup:`-1`]
1997 Estimated initial average error of the PMF for this bias. This value together with the
1998 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1999 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
2001 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
2002 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
2003 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
2004 then :mdp:`awh1-error-init` should reflect that knowledge.
2006 .. mdp:: awh1-growth
2008 .. mdp-value:: exp-linear
2010 Each bias keeps a reference weight histogram for the coordinate samples.
2011 Its size sets the magnitude of the bias function and free energy estimate updates
2012 (few samples corresponds to large updates and vice versa).
2013 Thus, its growth rate sets the maximum convergence rate.
2014 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
2015 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
2016 The initial stage is typically necessary for efficient convergence when starting a new simulation where
2017 high free energy barriers have not yet been flattened by the bias.
2019 .. mdp-value:: linear
2021 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
2022 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
2023 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
2025 .. mdp:: awh1-equilibrate-histogram
2029 Do not equilibrate histogram.
2033 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
2034 histogram of sampled weights is following the target distribution closely enough (specifically,
2035 at least 80% of the target region needs to have a local relative error of less than 20%). This
2036 option would typically only be used when :mdp:`awh1-share-group` > 0
2037 and the initial configurations poorly represent the target
2040 .. mdp:: awh1-target
2042 .. mdp-value:: constant
2044 The bias is tuned towards a constant (uniform) coordinate distribution
2045 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
2047 .. mdp-value:: cutoff
2049 Similar to :mdp-value:`awh1-target=constant`, but the target
2050 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
2051 where F is the free energy relative to the estimated global minimum.
2052 This provides a smooth switch of a flat target distribution in
2053 regions with free energy lower than the cut-off to a Boltzmann
2054 distribution in regions with free energy higher than the cut-off.
2056 .. mdp-value:: boltzmann
2058 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
2059 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
2060 would give the same coordinate distribution as sampling with a simulation temperature
2063 .. mdp-value:: local-boltzmann
2065 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
2066 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
2067 change of the bias only depends on the local sampling. This local convergence property is
2068 only compatible with :mdp-value:`awh1-growth=linear`, since for
2069 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
2071 .. mdp:: awh1-target-beta-scaling
2074 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
2075 it is the unitless beta scaling factor taking values in (0,1).
2077 .. mdp:: awh1-target-cutoff
2079 (0) [kJ mol\ :sup:`-1`]
2080 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
2082 .. mdp:: awh1-user-data
2086 Initialize the PMF and target distribution with default values.
2090 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
2091 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
2092 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
2093 The file name can be changed with the ``-awh`` option.
2094 The first :mdp:`awh1-ndim` columns of
2095 each input file should contain the coordinate values, such that each row defines a point in
2096 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
2097 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2098 be in the same column as written by :ref:`gmx awh`.
2100 .. mdp:: awh1-share-group
2104 Do not share the bias.
2106 .. mdp-value:: positive
2108 Share the bias and PMF estimates within and/or between simulations.
2109 Within a simulation, the bias will be shared between biases that have the
2110 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2111 With :mdp-value:`awh-share-multisim=yes` and
2112 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2113 Sharing may increase convergence initially, although the starting configurations
2114 can be critical, especially when sharing between many biases.
2115 Currently, positive group values should start at 1 and increase
2116 by 1 for each subsequent bias that is shared.
2121 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2122 The following options should be specified for each such dimension. Below only
2123 the options for dimension number 1 is shown. Options for other dimension indices are
2124 obtained by replacing '1' by the dimension index.
2126 .. mdp:: awh1-dim1-coord-provider
2130 The module providing the reaction coordinate for this dimension.
2131 Currently AWH can only act on pull coordinates.
2133 .. mdp:: awh1-dim1-coord-index
2136 Index of the pull coordinate defining this coordinate dimension.
2138 .. mdp:: awh1-dim1-force-constant
2140 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2141 Force constant for the (convolved) umbrella potential(s) along this
2142 coordinate dimension.
2144 .. mdp:: awh1-dim1-start
2147 Start value of the sampling interval along this dimension. The range of allowed
2148 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2149 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2150 is allowed. The interval will then wrap around from +period/2 to -period/2.
2151 For the direction geometry, the dimension is made periodic when
2152 the direction is along a box vector and covers more than 95%
2153 of the box length. Note that one should not apply pressure coupling
2154 along a periodic dimension.
2156 .. mdp:: awh1-dim1-end
2159 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2161 .. mdp:: awh1-dim1-diffusion
2163 (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps]
2164 Estimated diffusion constant for this coordinate dimension determining the initial
2165 biasing rate. This needs only be a rough estimate and should not critically
2166 affect the results unless it is set to something very low, leading to slow convergence,
2167 or very high, forcing the system far from equilibrium. Not setting this value
2168 explicitly generates a warning.
2170 .. mdp:: awh1-dim1-cover-diameter
2173 Diameter that needs to be sampled by a single simulation around a coordinate value
2174 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2175 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2176 across each coordinate value.
2177 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2178 (:mdp:`awh1-share-group`>0).
2179 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2180 for many sharing simulations does not guarantee transitions across free energy barriers.
2181 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2182 has independently sampled the whole interval.
2187 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2188 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2189 that can be used to achieve such a rotation.
2195 No enforced rotation will be applied. All enforced rotation options will
2196 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2201 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2202 under the :mdp:`rot-group0` option.
2204 .. mdp:: rot-ngroups
2207 Number of rotation groups.
2211 Name of rotation group 0 in the index file.
2216 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2217 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2218 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2223 Use mass weighted rotation group positions.
2228 Rotation vector, will get normalized.
2233 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2237 (0) [degree ps\ :sup:`-1`]
2238 Reference rotation rate of group 0.
2242 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2243 Force constant for group 0.
2245 .. mdp:: rot-slab-dist0
2248 Slab distance, if a flexible axis rotation type was chosen.
2250 .. mdp:: rot-min-gauss0
2253 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2254 (for the flexible axis potentials).
2258 (0.0001) [nm\ :sup:`2`]
2259 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2261 .. mdp:: rot-fit-method0
2264 Fitting method when determining the actual angle of a rotation group
2265 (can be one of ``rmsd``, ``norm``, or ``potential``).
2267 .. mdp:: rot-potfit-nsteps0
2270 For fit type ``potential``, the number of angular positions around the reference angle for which the
2271 rotation potential is evaluated.
2273 .. mdp:: rot-potfit-step0
2276 For fit type ``potential``, the distance in degrees between two angular positions.
2278 .. mdp:: rot-nstrout
2281 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2282 and the rotation potential energy.
2284 .. mdp:: rot-nstsout
2287 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2297 ignore distance restraint information in topology file
2299 .. mdp-value:: simple
2301 simple (per-molecule) distance restraints.
2303 .. mdp-value:: ensemble
2305 distance restraints over an ensemble of molecules in one
2306 simulation box. Normally, one would perform ensemble averaging
2307 over multiple simulations, using ``mdrun
2308 -multidir``. The environment
2309 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2310 within each ensemble (usually equal to the number of directories
2311 supplied to ``mdrun -multidir``).
2313 .. mdp:: disre-weighting
2315 .. mdp-value:: equal
2317 divide the restraint force equally over all atom pairs in the
2320 .. mdp-value:: conservative
2322 the forces are the derivative of the restraint potential, this
2323 results in an weighting of the atom pairs to the reciprocal
2324 seventh power of the displacement. The forces are conservative
2325 when :mdp:`disre-tau` is zero.
2327 .. mdp:: disre-mixed
2331 the violation used in the calculation of the restraint force is
2332 the time-averaged violation
2336 the violation used in the calculation of the restraint force is
2337 the square root of the product of the time-averaged violation
2338 and the instantaneous violation
2342 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2343 force constant for distance restraints, which is multiplied by a
2344 (possibly) different factor for each restraint given in the `fac`
2345 column of the interaction in the topology file.
2350 time constant for distance restraints running average. A value of
2351 zero turns off time averaging.
2353 .. mdp:: nstdisreout
2356 period between steps when the running time-averaged and
2357 instantaneous distances of all atom pairs involved in restraints
2358 are written to the energy file (can make the energy file very
2365 ignore orientation restraint information in topology file
2369 use orientation restraints, ensemble averaging can be performed
2370 with ``mdrun -multidir``
2374 (0) [kJ mol\ :sup:`-1`]
2375 force constant for orientation restraints, which is multiplied by a
2376 (possibly) different weight factor for each restraint, can be set
2377 to zero to obtain the orientations from a free simulation
2382 time constant for orientation restraints running average. A value
2383 of zero turns off time averaging.
2385 .. mdp:: orire-fitgrp
2387 fit group for orientation restraining. This group of atoms is used
2388 to determine the rotation **R** of the system with respect to the
2389 reference orientation. The reference orientation is the starting
2390 conformation of the first subsystem. For a protein, backbone is a
2393 .. mdp:: nstorireout
2396 period between steps when the running time-averaged and
2397 instantaneous orientations for all restraints, and the molecular
2398 order tensor are written to the energy file (can make the energy
2402 Free energy calculations
2403 ^^^^^^^^^^^^^^^^^^^^^^^^
2405 .. mdp:: free-energy
2409 Only use topology A.
2413 Interpolate between topology A (lambda=0) to topology B
2414 (lambda=1) and write the derivative of the Hamiltonian with
2415 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2416 or the Hamiltonian differences with respect to other lambda
2417 values (as specified with foreign lambda) to the energy file
2418 and/or to ``dhdl.xvg``, where they can be processed by, for
2419 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2420 are interpolated linearly as described in the manual. When
2421 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2422 used for the LJ and Coulomb interactions.
2426 Turns on expanded ensemble simulation, where the alchemical state
2427 becomes a dynamic variable, allowing jumping between different
2428 Hamiltonians. See the expanded ensemble options for controlling how
2429 expanded ensemble simulations are performed. The different
2430 Hamiltonians used in expanded ensemble simulations are defined by
2431 the other free energy options.
2433 .. mdp:: init-lambda
2436 starting value for lambda (float). Generally, this should only be
2437 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2438 other cases, :mdp:`init-lambda-state` should be specified
2439 instead. Must be greater than or equal to 0.
2441 .. mdp:: delta-lambda
2444 increment per time step for lambda
2446 .. mdp:: init-lambda-state
2449 starting value for the lambda state (integer). Specifies which
2450 columm of the lambda vector (:mdp:`coul-lambdas`,
2451 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2452 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2453 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2454 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2455 the first column, and so on.
2457 .. mdp:: fep-lambdas
2460 Zero, one or more lambda values for which Delta H values will be
2461 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2462 steps. Values must be between 0 and 1. Free energy differences
2463 between different lambda values can then be determined with
2464 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2465 other -lambdas keywords because all components of the lambda vector
2466 that are not specified will use :mdp:`fep-lambdas` (including
2467 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2469 .. mdp:: coul-lambdas
2472 Zero, one or more lambda values for which Delta H values will be
2473 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2474 steps. Values must be between 0 and 1. Only the electrostatic
2475 interactions are controlled with this component of the lambda
2476 vector (and only if the lambda=0 and lambda=1 states have differing
2477 electrostatic interactions).
2479 .. mdp:: vdw-lambdas
2482 Zero, one or more lambda values for which Delta H values will be
2483 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2484 steps. Values must be between 0 and 1. Only the van der Waals
2485 interactions are controlled with this component of the lambda
2488 .. mdp:: bonded-lambdas
2491 Zero, one or more lambda values for which Delta H values will be
2492 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2493 steps. Values must be between 0 and 1. Only the bonded interactions
2494 are controlled with this component of the lambda vector.
2496 .. mdp:: restraint-lambdas
2499 Zero, one or more lambda values for which Delta H values will be
2500 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2501 steps. Values must be between 0 and 1. Only the restraint
2502 interactions: dihedral restraints, and the pull code restraints are
2503 controlled with this component of the lambda vector.
2505 .. mdp:: mass-lambdas
2508 Zero, one or more lambda values for which Delta H values will be
2509 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2510 steps. Values must be between 0 and 1. Only the particle masses are
2511 controlled with this component of the lambda vector.
2513 .. mdp:: temperature-lambdas
2516 Zero, one or more lambda values for which Delta H values will be
2517 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2518 steps. Values must be between 0 and 1. Only the temperatures
2519 controlled with this component of the lambda vector. Note that
2520 these lambdas should not be used for replica exchange, only for
2521 simulated tempering.
2523 .. mdp:: calc-lambda-neighbors
2526 Controls the number of lambda values for which Delta H values will
2527 be calculated and written out, if :mdp:`init-lambda-state` has
2528 been set. A positive value will limit the number of lambda points
2529 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2530 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2531 has a value of 2, energies for lambda points 3-7 will be calculated
2532 and writen out. A value of -1 means all lambda points will be
2533 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2534 1 is sufficient, while for MBAR -1 should be used.
2539 the soft-core alpha parameter, a value of 0 results in linear
2540 interpolation of the LJ and Coulomb interactions
2545 the power of the radial term in the soft-core equation. Possible
2546 values are 6 and 48. 6 is more standard, and is the default. When
2547 48 is used, then sc-alpha should generally be much lower (between
2553 Whether to apply the soft-core free energy interaction
2554 transformation to the Columbic interaction of a molecule. Default
2555 is no, as it is generally more efficient to turn off the Coulomic
2556 interactions linearly before turning off the van der Waals
2557 interactions. Note that it is only taken into account when lambda
2558 states are used, not with :mdp:`couple-lambda0` /
2559 :mdp:`couple-lambda1`, and you can still turn off soft-core
2560 interactions by setting :mdp:`sc-alpha` to 0.
2565 the power for lambda in the soft-core function, only the values 1
2571 the soft-core sigma for particles which have a C6 or C12 parameter
2572 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2574 .. mdp:: couple-moltype
2576 Here one can supply a molecule type (as defined in the topology)
2577 for calculating solvation or coupling free energies. There is a
2578 special option ``system`` that couples all molecule types in the
2579 system. This can be useful for equilibrating a system starting from
2580 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2581 on. The Van der Waals interactions and/or charges in this molecule
2582 type can be turned on or off between lambda=0 and lambda=1,
2583 depending on the settings of :mdp:`couple-lambda0` and
2584 :mdp:`couple-lambda1`. If you want to decouple one of several
2585 copies of a molecule, you need to copy and rename the molecule
2586 definition in the topology.
2588 .. mdp:: couple-lambda0
2590 .. mdp-value:: vdw-q
2592 all interactions are on at lambda=0
2596 the charges are zero (no Coulomb interactions) at lambda=0
2600 the Van der Waals interactions are turned at lambda=0; soft-core
2601 interactions will be required to avoid singularities
2605 the Van der Waals interactions are turned off and the charges
2606 are zero at lambda=0; soft-core interactions will be required to
2607 avoid singularities.
2609 .. mdp:: couple-lambda1
2611 analogous to :mdp:`couple-lambda1`, but for lambda=1
2613 .. mdp:: couple-intramol
2617 All intra-molecular non-bonded interactions for moleculetype
2618 :mdp:`couple-moltype` are replaced by exclusions and explicit
2619 pair interactions. In this manner the decoupled state of the
2620 molecule corresponds to the proper vacuum state without
2621 periodicity effects.
2625 The intra-molecular Van der Waals and Coulomb interactions are
2626 also turned on/off. This can be useful for partitioning
2627 free-energies of relatively large molecules, where the
2628 intra-molecular non-bonded interactions might lead to
2629 kinetically trapped vacuum conformations. The 1-4 pair
2630 interactions are not turned off.
2635 the frequency for writing dH/dlambda and possibly Delta H to
2636 dhdl.xvg, 0 means no ouput, should be a multiple of
2637 :mdp:`nstcalcenergy`.
2639 .. mdp:: dhdl-derivatives
2643 If yes (the default), the derivatives of the Hamiltonian with
2644 respect to lambda at each :mdp:`nstdhdl` step are written
2645 out. These values are needed for interpolation of linear energy
2646 differences with :ref:`gmx bar` (although the same can also be
2647 achieved with the right foreign lambda setting, that may not be as
2648 flexible), or with thermodynamic integration
2650 .. mdp:: dhdl-print-energy
2654 Include either the total or the potential energy in the dhdl
2655 file. Options are 'no', 'potential', or 'total'. This information
2656 is needed for later free energy analysis if the states of interest
2657 are at different temperatures. If all states are at the same
2658 temperature, this information is not needed. 'potential' is useful
2659 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2660 file. When rerunning from an existing trajectory, the kinetic
2661 energy will often not be correct, and thus one must compute the
2662 residual free energy from the potential alone, with the kinetic
2663 energy component computed analytically.
2665 .. mdp:: separate-dhdl-file
2669 The free energy values that are calculated (as specified with
2670 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2671 written out to a separate file, with the default name
2672 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2677 The free energy values are written out to the energy output file
2678 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2679 steps), where they can be extracted with :ref:`gmx energy` or
2680 used directly with :ref:`gmx bar`.
2682 .. mdp:: dh-hist-size
2685 If nonzero, specifies the size of the histogram into which the
2686 Delta H values (specified with foreign lambda) and the derivative
2687 dH/dl values are binned, and written to ener.edr. This can be used
2688 to save disk space while calculating free energy differences. One
2689 histogram gets written for each foreign lambda and two for the
2690 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2691 histogram settings (too small size or too wide bins) can introduce
2692 errors. Do not use histograms unless you're certain you need it.
2694 .. mdp:: dh-hist-spacing
2697 Specifies the bin width of the histograms, in energy units. Used in
2698 conjunction with :mdp:`dh-hist-size`. This size limits the
2699 accuracy with which free energies can be calculated. Do not use
2700 histograms unless you're certain you need it.
2703 Expanded Ensemble calculations
2704 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2706 .. mdp:: nstexpanded
2708 The number of integration steps beween attempted moves changing the
2709 system Hamiltonian in expanded ensemble simulations. Must be a
2710 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2717 No Monte Carlo in state space is performed.
2719 .. mdp-value:: metropolis-transition
2721 Uses the Metropolis weights to update the expanded ensemble
2722 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2725 .. mdp-value:: barker-transition
2727 Uses the Barker transition critera to update the expanded
2728 ensemble weight of each state i, defined by exp(-beta_new
2729 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2731 .. mdp-value:: wang-landau
2733 Uses the Wang-Landau algorithm (in state space, not energy
2734 space) to update the expanded ensemble weights.
2736 .. mdp-value:: min-variance
2738 Uses the minimum variance updating method of Escobedo et al. to
2739 update the expanded ensemble weights. Weights will not be the
2740 free energies, but will rather emphasize states that need more
2741 sampling to give even uncertainty.
2743 .. mdp:: lmc-mc-move
2747 No Monte Carlo in state space is performed.
2749 .. mdp-value:: metropolis-transition
2751 Randomly chooses a new state up or down, then uses the
2752 Metropolis critera to decide whether to accept or reject:
2753 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2755 .. mdp-value:: barker-transition
2757 Randomly chooses a new state up or down, then uses the Barker
2758 transition critera to decide whether to accept or reject:
2759 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2761 .. mdp-value:: gibbs
2763 Uses the conditional weights of the state given the coordinate
2764 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2767 .. mdp-value:: metropolized-gibbs
2769 Uses the conditional weights of the state given the coordinate
2770 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2771 to move to, EXCLUDING the current state, then uses a rejection
2772 step to ensure detailed balance. Always more efficient that
2773 Gibbs, though only marginally so in many situations, such as
2774 when only the nearest neighbors have decent phase space
2780 random seed to use for Monte Carlo moves in state space. When
2781 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2783 .. mdp:: mc-temperature
2785 Temperature used for acceptance/rejection for Monte Carlo moves. If
2786 not specified, the temperature of the simulation specified in the
2787 first group of :mdp:`ref-t` is used.
2792 The cutoff for the histogram of state occupancies to be reset, and
2793 the free energy incrementor to be changed from delta to delta *
2794 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2795 each histogram) / (average number of samples at each
2796 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2797 histogram is only considered flat if all Nratio > 0.8 AND
2798 simultaneously all 1/Nratio > 0.8.
2803 Each time the histogram is considered flat, then the current value
2804 of the Wang-Landau incrementor for the free energies is multiplied
2805 by :mdp:`wl-scale`. Value must be between 0 and 1.
2807 .. mdp:: init-wl-delta
2810 The initial value of the Wang-Landau incrementor in kT. Some value
2811 near 1 kT is usually most efficient, though sometimes a value of
2812 2-3 in units of kT works better if the free energy differences are
2815 .. mdp:: wl-oneovert
2818 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2819 the large sample limit. There is significant evidence that the
2820 standard Wang-Landau algorithms in state space presented here
2821 result in free energies getting 'burned in' to incorrect values
2822 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2823 then when the incrementor becomes less than 1/N, where N is the
2824 mumber of samples collected (and thus proportional to the data
2825 collection time, hence '1 over t'), then the Wang-Lambda
2826 incrementor is set to 1/N, decreasing every step. Once this occurs,
2827 :mdp:`wl-ratio` is ignored, but the weights will still stop
2828 updating when the equilibration criteria set in
2829 :mdp:`lmc-weights-equil` is achieved.
2831 .. mdp:: lmc-repeats
2834 Controls the number of times that each Monte Carlo swap type is
2835 performed each iteration. In the limit of large numbers of Monte
2836 Carlo repeats, then all methods converge to Gibbs sampling. The
2837 value will generally not need to be different from 1.
2839 .. mdp:: lmc-gibbsdelta
2842 Limit Gibbs sampling to selected numbers of neighboring states. For
2843 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2844 sampling over all of the states that are defined. A positive value
2845 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2846 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2847 value of -1 means that all states are considered. For less than 100
2848 states, it is probably not that expensive to include all states.
2850 .. mdp:: lmc-forced-nstart
2853 Force initial state space sampling to generate weights. In order to
2854 come up with reasonable initial weights, this setting allows the
2855 simulation to drive from the initial to the final lambda state,
2856 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2857 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2858 sufficiently long (thousands of steps, perhaps), then the weights
2859 will be close to correct. However, in most cases, it is probably
2860 better to simply run the standard weight equilibration algorithms.
2862 .. mdp:: nst-transition-matrix
2865 Frequency of outputting the expanded ensemble transition matrix. A
2866 negative number means it will only be printed at the end of the
2869 .. mdp:: symmetrized-transition-matrix
2872 Whether to symmetrize the empirical transition matrix. In the
2873 infinite limit the matrix will be symmetric, but will diverge with
2874 statistical noise for short timescales. Forced symmetrization, by
2875 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2876 like the existence of (small magnitude) negative eigenvalues.
2878 .. mdp:: mininum-var-min
2881 The min-variance strategy (option of :mdp:`lmc-stats` is only
2882 valid for larger number of samples, and can get stuck if too few
2883 samples are used at each state. :mdp:`mininum-var-min` is the
2884 minimum number of samples that each state that are allowed before
2885 the min-variance strategy is activated if selected.
2887 .. mdp:: init-lambda-weights
2889 The initial weights (free energies) used for the expanded ensemble
2890 states. Default is a vector of zero weights. format is similar to
2891 the lambda vector settings in :mdp:`fep-lambdas`, except the
2892 weights can be any floating point number. Units are kT. Its length
2893 must match the lambda vector lengths.
2895 .. mdp:: lmc-weights-equil
2899 Expanded ensemble weights continue to be updated throughout the
2904 The input expanded ensemble weights are treated as equilibrated,
2905 and are not updated throughout the simulation.
2907 .. mdp-value:: wl-delta
2909 Expanded ensemble weight updating is stopped when the
2910 Wang-Landau incrementor falls below this value.
2912 .. mdp-value:: number-all-lambda
2914 Expanded ensemble weight updating is stopped when the number of
2915 samples at all of the lambda states is greater than this value.
2917 .. mdp-value:: number-steps
2919 Expanded ensemble weight updating is stopped when the number of
2920 steps is greater than the level specified by this value.
2922 .. mdp-value:: number-samples
2924 Expanded ensemble weight updating is stopped when the number of
2925 total samples across all lambda states is greater than the level
2926 specified by this value.
2928 .. mdp-value:: count-ratio
2930 Expanded ensemble weight updating is stopped when the ratio of
2931 samples at the least sampled lambda state and most sampled
2932 lambda state greater than this value.
2934 .. mdp:: simulated-tempering
2937 Turn simulated tempering on or off. Simulated tempering is
2938 implemented as expanded ensemble sampling with different
2939 temperatures instead of different Hamiltonians.
2941 .. mdp:: sim-temp-low
2944 Low temperature for simulated tempering.
2946 .. mdp:: sim-temp-high
2949 High temperature for simulated tempering.
2951 .. mdp:: simulated-tempering-scaling
2953 Controls the way that the temperatures at intermediate lambdas are
2954 calculated from the :mdp:`temperature-lambdas` part of the lambda
2957 .. mdp-value:: linear
2959 Linearly interpolates the temperatures using the values of
2960 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2961 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2962 a temperature of 350. A nonlinear set of temperatures can always
2963 be implemented with uneven spacing in lambda.
2965 .. mdp-value:: geometric
2967 Interpolates temperatures geometrically between
2968 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2969 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2970 :mdp:`sim-temp-low`) raised to the power of
2971 (i/(ntemps-1)). This should give roughly equal exchange for
2972 constant heat capacity, though of course things simulations that
2973 involve protein folding have very high heat capacity peaks.
2975 .. mdp-value:: exponential
2977 Interpolates temperatures exponentially between
2978 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2979 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2980 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2981 (i))-1)/(exp(1.0)-i)).
2989 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2990 in groups Protein and Sol will experience constant acceleration as
2991 specified in the :mdp:`accelerate` line
2995 (0) [nm ps\ :sup:`-2`]
2996 acceleration for :mdp:`acc-grps`; x, y and z for each group
2997 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2998 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
3003 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
3004 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
3005 specifies for which dimension(s) the freezing applies. To avoid
3006 spurious contributions to the virial and pressure due to large
3007 forces between completely frozen atoms you need to use energy group
3008 exclusions, this also saves computing time. Note that coordinates
3009 of frozen atoms are not scaled by pressure-coupling algorithms.
3013 dimensions for which groups in :mdp:`freezegrps` should be frozen,
3014 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
3015 N N N N`` means that particles in the first group can move only in
3016 Z direction. The particles in the second group can move in any
3019 .. mdp:: cos-acceleration
3021 (0) [nm ps\ :sup:`-2`]
3022 the amplitude of the acceleration profile for calculating the
3023 viscosity. The acceleration is in the X-direction and the magnitude
3024 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
3025 added to the energy file: the amplitude of the velocity profile and
3030 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
3031 The velocities of deformation for the box elements: a(x) b(y) c(z)
3032 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
3033 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
3034 elements are corrected for periodicity. The coordinates are
3035 transformed accordingly. Frozen degrees of freedom are (purposely)
3036 also transformed. The time ts is set to t at the first step and at
3037 steps at which x and v are written to trajectory to ensure exact
3038 restarts. Deformation can be used together with semiisotropic or
3039 anisotropic pressure coupling when the appropriate
3040 compressibilities are set to zero. The diagonal elements can be
3041 used to strain a solid. The off-diagonal elements can be used to
3042 shear a solid or a liquid.
3048 .. mdp:: electric-field-x
3049 .. mdp:: electric-field-y
3050 .. mdp:: electric-field-z
3052 Here you can specify an electric field that optionally can be
3053 alternating and pulsed. The general expression for the field
3054 has the form of a gaussian laser pulse:
3056 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
3058 For example, the four parameters for direction x are set in the
3059 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
3060 and ``electric-field-z``) like
3062 ``electric-field-x = E0 omega t0 sigma``
3064 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
3066 In the special case that ``sigma = 0``, the exponential term is omitted
3067 and only the cosine term is used. If also ``omega = 0`` a static
3068 electric field is applied.
3070 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
3073 Mixed quantum/classical molecular dynamics
3074 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3084 Do a QM/MM simulation. Several groups can be described at
3085 different QM levels separately. These are specified in the
3086 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
3087 initio* theory at which the groups are described is specified by
3088 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
3089 groups at different levels of theory is only possible with the
3090 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
3094 groups to be descibed at the QM level (works also in case of MiMiC QM/MM)
3098 .. mdp-value:: normal
3100 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
3101 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
3102 *ab initio* theory. The rest of the system is described at the
3103 MM level. The QM and MM subsystems interact as follows: MM point
3104 charges are included in the QM one-electron hamiltonian and all
3105 Lennard-Jones interactions are described at the MM level.
3107 .. mdp-value:: ONIOM
3109 The interaction between the subsystem is described using the
3110 ONIOM method by Morokuma and co-workers. There can be more than
3111 one :mdp:`QMMM-grps` each modeled at a different level of QM
3112 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
3117 Method used to compute the energy and gradients on the QM
3118 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
3119 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
3120 included in the active space is specified by :mdp:`CASelectrons`
3121 and :mdp:`CASorbitals`.
3126 Basis set used to expand the electronic wavefuntion. Only Gaussian
3127 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3128 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
3133 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
3134 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
3135 layer needs to be specified separately.
3140 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
3141 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
3142 needs to be specified separately.
3144 .. mdp:: CASorbitals
3147 The number of orbitals to be included in the active space when
3148 doing a CASSCF computation.
3150 .. mdp:: CASelectrons
3153 The number of electrons to be included in the active space when
3154 doing a CASSCF computation.
3160 No surface hopping. The system is always in the electronic
3165 Do a QM/MM MD simulation on the excited state-potential energy
3166 surface and enforce a *diabatic* hop to the ground-state when
3167 the system hits the conical intersection hyperline in the course
3168 the simulation. This option only works in combination with the
3172 Computational Electrophysiology
3173 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3174 Use these options to switch on and control ion/water position exchanges in "Computational
3175 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3181 Do not enable ion/water position exchanges.
3183 .. mdp-value:: X ; Y ; Z
3185 Allow for ion/water position exchanges along the chosen direction.
3186 In a typical setup with the membranes parallel to the x-y plane,
3187 ion/water pairs need to be exchanged in Z direction to sustain the
3188 requested ion concentrations in the compartments.
3190 .. mdp:: swap-frequency
3192 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3193 per compartment are determined and exchanges made if necessary.
3194 Normally it is not necessary to check at every time step.
3195 For typical Computational Electrophysiology setups, a value of about 100 is
3196 sufficient and yields a negligible performance impact.
3198 .. mdp:: split-group0
3200 Name of the index group of the membrane-embedded part of channel #0.
3201 The center of mass of these atoms defines one of the compartment boundaries
3202 and should be chosen such that it is near the center of the membrane.
3204 .. mdp:: split-group1
3206 Channel #1 defines the position of the other compartment boundary.
3208 .. mdp:: massw-split0
3210 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3214 Use the geometrical center.
3218 Use the center of mass.
3220 .. mdp:: massw-split1
3222 (no) As above, but for split-group #1.
3224 .. mdp:: solvent-group
3226 Name of the index group of solvent molecules.
3228 .. mdp:: coupl-steps
3230 (10) Average the number of ions per compartment over these many swap attempt steps.
3231 This can be used to prevent that ions near a compartment boundary
3232 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3236 (1) The number of different ion types to be controlled. These are during the
3237 simulation exchanged with solvent molecules to reach the desired reference numbers.
3239 .. mdp:: iontype0-name
3241 Name of the first ion type.
3243 .. mdp:: iontype0-in-A
3245 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3246 The default value of -1 means: use the number of ions as found in time step 0
3249 .. mdp:: iontype0-in-B
3251 (-1) Reference number of ions of type 0 for compartment B.
3253 .. mdp:: bulk-offsetA
3255 (0.0) Offset of the first swap layer from the compartment A midplane.
3256 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3257 at maximum distance (= bulk concentration) to the split group layers. However,
3258 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3259 towards one of the compartment-partitioning layers (at +/- 1.0).
3261 .. mdp:: bulk-offsetB
3263 (0.0) Offset of the other swap layer from the compartment B midplane.
3268 (\1) Only swap ions if threshold difference to requested count is reached.
3272 (2.0) [nm] Radius of the split cylinder #0.
3273 Two split cylinders (mimicking the channel pores) can optionally be defined
3274 relative to the center of the split group. With the help of these cylinders
3275 it can be counted which ions have passed which channel. The split cylinder
3276 definition has no impact on whether or not ion/water swaps are done.
3280 (1.0) [nm] Upper extension of the split cylinder #0.
3284 (1.0) [nm] Lower extension of the split cylinder #0.
3288 (2.0) [nm] Radius of the split cylinder #1.
3292 (1.0) [nm] Upper extension of the split cylinder #1.
3296 (1.0) [nm] Lower extension of the split cylinder #1.
3299 User defined thingies
3300 ^^^^^^^^^^^^^^^^^^^^^
3304 .. mdp:: userint1 (0)
3305 .. mdp:: userint2 (0)
3306 .. mdp:: userint3 (0)
3307 .. mdp:: userint4 (0)
3308 .. mdp:: userreal1 (0)
3309 .. mdp:: userreal2 (0)
3310 .. mdp:: userreal3 (0)
3311 .. mdp:: userreal4 (0)
3313 These you can use if you modify code. You can pass integers and
3314 reals and groups to your subroutine. Check the inputrec definition
3315 in ``src/gromacs/mdtypes/inputrec.h``
3320 These features have been removed from |Gromacs|, but so that old
3321 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3322 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3323 fatal error if this is set.
3329 .. mdp:: implicit-solvent
3333 .. _reference manual: gmx-manual-parent-dir_