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 ============================================
14 Default values are given in parentheses, or listed first among
15 choices. The first option in the list is always the default
16 option. Units are given in square brackets The difference between a
17 dash and an underscore is ignored.
19 A :ref:`sample mdp file <mdp>` is available. This should be
20 appropriate to start a normal simulation. Edit it to suit your
21 specific needs and desires.
29 directories to include in your topology. Format:
30 ``-I/home/john/mylib -I../otherlib``
34 defines to pass to the preprocessor, default is no defines. You can
35 use any defines to control options in your customized topology
36 files. Options that act on existing :ref:`top` file mechanisms
39 ``-DFLEXIBLE`` will use flexible water instead of rigid water
40 into your topology, this can be useful for normal mode analysis.
42 ``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
43 your topology, used for implementing position restraints.
51 (Despite the name, this list includes algorithms that are not
52 actually integrators over time. :mdp-value:`integrator=steep` and
53 all entries following it are in this category)
57 A leap-frog algorithm for integrating Newton's equations of motion.
61 A velocity Verlet algorithm for integrating Newton's equations
62 of motion. For constant NVE simulations started from
63 corresponding points in the same trajectory, the trajectories
64 are analytically, but not binary, identical to the
65 :mdp-value:`integrator=md` leap-frog integrator. The the kinetic
66 energy, which is determined from the whole step velocities and
67 is therefore slightly too high. The advantage of this integrator
68 is more accurate, reversible Nose-Hoover and Parrinello-Rahman
69 coupling integration based on Trotter expansion, as well as
70 (slightly too small) full step velocity output. This all comes
71 at the cost off extra computation, especially with constraints
72 and extra communication in parallel. Note that for nearly all
73 production simulations the :mdp-value:`integrator=md` integrator
76 .. mdp-value:: md-vv-avek
78 A velocity Verlet algorithm identical to
79 :mdp-value:`integrator=md-vv`, except that the kinetic energy is
80 determined as the average of the two half step kinetic energies
81 as in the :mdp-value:`integrator=md` integrator, and this thus
82 more accurate. With Nose-Hoover and/or Parrinello-Rahman
83 coupling this comes with a slight increase in computational
88 An accurate and efficient leap-frog stochastic dynamics
89 integrator. With constraints, coordinates needs to be
90 constrained twice per integration step. Depending on the
91 computational cost of the force calculation, this can take a
92 significant part of the simulation time. The temperature for one
93 or more groups of atoms (:mdp:`tc-grps`) is set with
94 :mdp:`ref-t`, the inverse friction constant for each group is
95 set with :mdp:`tau-t`. The parameter :mdp:`tcoupl` is
96 ignored. The random generator is initialized with
97 :mdp:`ld-seed`. When used as a thermostat, an appropriate value
98 for :mdp:`tau-t` is 2 ps, since this results in a friction that
99 is lower than the internal friction of water, while it is high
100 enough to remove excess heat NOTE: temperature deviations decay
101 twice as fast as with a Berendsen thermostat with the same
106 This used to be the default sd integrator, but is now
107 deprecated. Four Gaussian random numbers are required per
108 coordinate per step. With constraints, the temperature will be
113 An Euler integrator for Brownian or position Langevin dynamics,
114 the velocity is the force divided by a friction coefficient
115 (:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
116 :mdp:`bd-fric` is 0, the friction coefficient for each particle
117 is calculated as mass/ :mdp:`tau-t`, as for the integrator
118 :mdp-value:`integrator=sd`. The random generator is initialized
123 A steepest descent algorithm for energy minimization. The
124 maximum step size is :mdp:`emstep`, the tolerance is
129 A conjugate gradient algorithm for energy minimization, the
130 tolerance is :mdp:`emtol`. CG is more efficient when a steepest
131 descent step is done every once in a while, this is determined
132 by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
133 analysis, which requires a very high accuracy, |Gromacs| should be
134 compiled in double precision.
136 .. mdp-value:: l-bfgs
138 A quasi-Newtonian algorithm for energy minimization according to
139 the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
140 practice this seems to converge faster than Conjugate Gradients,
141 but due to the correction steps necessary it is not (yet)
146 Normal mode analysis is performed on the structure in the :ref:`tpr`
147 file. |Gromacs| should be compiled in double precision.
151 Test particle insertion. The last molecule in the topology is
152 the test particle. A trajectory must be provided to ``mdrun
153 -rerun``. This trajectory should not contain the molecule to be
154 inserted. Insertions are performed :mdp:`nsteps` times in each
155 frame at random locations and with random orientiations of the
156 molecule. When :mdp:`nstlist` is larger than one,
157 :mdp:`nstlist` insertions are performed in a sphere with radius
158 :mdp:`rtpi` around a the same random location using the same
159 neighborlist (and the same long-range energy when :mdp:`rvdw`
160 or :mdp:`rcoulomb` > :mdp:`rlist`, which is only allowed for
161 single-atom molecules). Since neighborlist construction is
162 expensive, one can perform several extra insertions with the
163 same list almost for free. The random seed is set with
164 :mdp:`ld-seed`. The temperature for the Boltzmann weighting is
165 set with :mdp:`ref-t`, this should match the temperature of the
166 simulation of the original trajectory. Dispersion correction is
167 implemented correctly for TPI. All relevant quantities are
168 written to the file specified with ``mdrun -tpi``. The
169 distribution of insertion energies is written to the file
170 specified with ``mdrun -tpid``. No trajectory or energy file is
171 written. Parallel TPI gives identical results to single-node
172 TPI. For charged molecules, using PME with a fine grid is most
173 accurate and also efficient, since the potential in the system
174 only needs to be calculated once per frame.
178 Test particle insertion into a predefined cavity location. The
179 procedure is the same as for :mdp-value:`integrator=tpi`, except
180 that one coordinate extra is read from the trajectory, which is
181 used as the insertion location. The molecule to be inserted
182 should be centered at 0,0,0. |Gromacs| does not do this for you,
183 since for different situations a different way of centering
184 might be optimal. Also :mdp:`rtpi` sets the radius for the
185 sphere around this location. Neighbor searching is done only
186 once per frame, :mdp:`nstlist` is not used. Parallel
187 :mdp-value:`integrator=tpic` gives identical results to
188 single-rank :mdp-value:`integrator=tpic`.
193 starting time for your run (only makes sense for time-based
199 time step for integration (only makes sense for time-based
205 maximum number of steps to integrate or minimize, -1 is no
211 The starting step. The time at an step i in a run is
212 calculated as: t = :mdp:`tinit` + :mdp:`dt` *
213 (:mdp:`init-step` + i). The free-energy lambda is calculated
214 as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
215 (:mdp:`init-step` + i). Also non-equilibrium MD parameters can
216 depend on the step number. Thus for exact restarts or redoing
217 part of a run it might be necessary to set :mdp:`init-step` to
218 the step number of the restart frame. :ref:`gmx convert-tpr`
219 does this automatically.
223 .. mdp-value:: Linear
225 Remove center of mass translation
227 .. mdp-value:: Angular
229 Remove center of mass translation and rotation around the center of mass
233 No restriction on the center of mass motion
238 frequency for center of mass motion removal
242 group(s) for center of mass motion removal, default is the whole
252 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
253 the friction coefficient for each particle is calculated as mass/
259 used to initialize random generator for thermal noise for
260 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
261 a pseudo random seed is used. When running BD or SD on multiple
262 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
263 the processor number.
271 (10.0) \[kJ mol-1 nm-1\]
272 the minimization is converged when the maximum force is smaller
283 frequency of performing 1 steepest descent step while doing
284 conjugate gradient energy minimization.
289 Number of correction steps to use for L-BFGS minimization. A higher
290 number is (at least theoretically) more accurate, but slower.
293 Shell Molecular Dynamics
294 ^^^^^^^^^^^^^^^^^^^^^^^^
296 When shells or flexible constraints are present in the system the
297 positions of the shells and the lengths of the flexible constraints
298 are optimized at every time step until either the RMS force on the
299 shells and constraints is less than :mdp:`emtol`, or a maximum number
300 of iterations :mdp:`niter` has been reached. Minimization is converged
301 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
302 value should be 1.0 at most.
307 maximum number of iterations for optimizing the shell positions and
308 the flexible constraints.
313 the step size for optimizing the flexible constraints. Should be
314 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
315 particles in a flexible constraint and d2V/dq2 is the second
316 derivative of the potential in the constraint direction. Hopefully
317 this number does not differ too much between the flexible
318 constraints, as the number of iterations and thus the runtime is
319 very sensitive to fcstep. Try several values!
322 Test particle insertion
323 ^^^^^^^^^^^^^^^^^^^^^^^
328 the test particle insertion radius, see integrators
329 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
338 number of steps that elapse between writing coordinates to output
339 trajectory file, the last coordinates are always written
344 number of steps that elapse between writing velocities to output
345 trajectory, the last velocities are always written
350 number of steps that elapse between writing forces to output
356 number of steps that elapse between writing energies to the log
357 file, the last energies are always written
359 .. mdp:: nstcalcenergy
362 number of steps that elapse between calculating the energies, 0 is
363 never. This option is only relevant with dynamics. With a
364 twin-range cut-off setup :mdp:`nstcalcenergy` should be equal to
365 or a multiple of :mdp:`nstlist`. This option affects the
366 performance in parallel simulations, because calculating energies
367 requires global communication between all processes which can
368 become a bottleneck at high parallelization.
373 number of steps that else between writing energies to energy file,
374 the last energies are always written, should be a multiple of
375 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
376 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
377 energy file, so :ref:`gmx energy` can report exact energy averages
378 and fluctuations also when :mdp:`nstenergy` > 1
380 .. mdp:: nstxout-compressed
383 number of steps that elapse between writing position coordinates
384 using lossy compression
386 .. mdp:: compressed-x-precision
389 precision with which to write to the compressed trajectory file
391 .. mdp:: compressed-x-grps
393 group(s) to write to the compressed trajectory file, by default the
394 whole system is written (if :mdp:`nstxout-compressed` > 0)
398 group(s) for which to write to write short-ranged non-bonded
399 potential energies to the energy file (not supported on GPUs)
405 .. mdp:: cutoff-scheme
407 .. mdp-value:: Verlet
409 Generate a pair list with buffering. The buffer size is
410 automatically set based on :mdp:`verlet-buffer-tolerance`,
411 unless this is set to -1, in which case :mdp:`rlist` will be
412 used. This option has an explicit, exact cut-off at :mdp:`rvdw`
413 equal to :mdp:`rcoulomb`. Currently only cut-off,
414 reaction-field, PME electrostatics and plain LJ are
415 supported. Some :ref:`gmx mdrun` functionality is not yet
416 supported with the :mdp:`Verlet` scheme, but :ref:`gmx grompp`
417 checks for this. Native GPU acceleration is only supported with
418 :mdp:`Verlet`. With GPU-accelerated PME or with separate PME
419 ranks, :ref:`gmx mdrun` will automatically tune the CPU/GPU load
420 balance by scaling :mdp:`rcoulomb` and the grid spacing. This
421 can be turned off with ``mdrun -notunepme``. :mdp:`Verlet` is
422 faster than :mdp:`group` when there is no water, or if
423 :mdp:`group` would use a pair-list buffer to conserve energy.
427 Generate a pair list for groups of atoms. These groups
428 correspond to the charge groups in the topology. This was the
429 only cut-off treatment scheme before version 4.6, and is
430 **deprecated in |gmx-version|**. There is no explicit buffering of
431 the pair list. This enables efficient force calculations for
432 water, but energy is only conserved when a buffer is explicitly
441 Frequency to update the neighbor list (and the long-range
442 forces, when using twin-range cut-offs). When this is 0, the
443 neighbor list is made only once. With energy minimization the
444 neighborlist will be updated for every energy evaluation when
445 :mdp:`nstlist` is greater than 0. With :mdp:`Verlet` and
446 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
447 a minimum value and :ref:`gmx mdrun` might increase it, unless
448 it is set to 1. With parallel simulations and/or non-bonded
449 force calculation on the GPU, a value of 20 or 40 often gives
450 the best performance. With :mdp:`group` and non-exact
451 cut-off's, :mdp:`nstlist` will affect the accuracy of your
452 simulation and it can not be chosen freely.
456 The neighbor list is only constructed once and never
457 updated. This is mainly useful for vacuum simulations in which
458 all particles see each other.
467 Controls the period between calculations of long-range forces when
468 using the group cut-off scheme.
472 Calculate the long-range forces every single step. This is
473 useful to have separate neighbor lists with buffers for
474 electrostatics and Van der Waals interactions, and in particular
475 it makes it possible to have the Van der Waals cutoff longer
476 than electrostatics (useful *e.g.* with PME). However, there is
477 no point in having identical long-range cutoffs for both
478 interaction forms and update them every step - then it will be
479 slightly faster to put everything in the short-range list.
483 Calculate the long-range forces every :mdp:`nstcalclr` steps
484 and use a multiple-time-step integrator to combine forces. This
485 can now be done more frequently than :mdp:`nstlist` since the
486 lists are stored, and it might be a good idea *e.g.* for Van der
487 Waals interactions that vary slower than electrostatics.
491 Calculate long-range forces on steps where neighbor searching is
492 performed. While this is the default value, you might want to
493 consider updating the long-range forces more frequently.
495 Note that twin-range force evaluation might be enabled
496 automatically by PP-PME load balancing. This is done in order to
497 maintain the chosen Van der Waals interaction radius even if the
498 load balancing is changing the electrostatics cutoff. If the
499 :ref:`mdp` file already specifies twin-range interactions (*e.g.* to
500 evaluate Lennard-Jones interactions with a longer cutoff than
501 the PME electrostatics every 2-3 steps), the load balancing will
502 have also a small effect on Lennard-Jones, since the short-range
503 cutoff (inside which forces are evaluated every step) is
510 Make a grid in the box and only check atoms in neighboring grid
511 cells when constructing a new neighbor list every
512 :mdp:`nstlist` steps. In large systems grid search is much
513 faster than simple search.
515 .. mdp-value:: simple
517 Check every atom in the box when constructing a new neighbor
518 list every :mdp:`nstlist` steps (only with :mdp:`group`
525 Use periodic boundary conditions in all directions.
529 Use no periodic boundary conditions, ignore the box. To simulate
530 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
531 best performance without cut-offs on a single MPI rank, set
532 :mdp:`nstlist` to zero and :mdp:`ns-type` =simple.
536 Use periodic boundary conditions in x and y directions
537 only. This works only with :mdp:`ns-type` =grid and can be used
538 in combination with walls_. Without walls or with only one wall
539 the system size is infinite in the z direction. Therefore
540 pressure coupling or Ewald summation methods can not be
541 used. These disadvantages do not apply when two walls are used.
543 .. mdp:: periodic-molecules
547 molecules are finite, fast molecular PBC can be used
551 for systems with molecules that couple to themselves through the
552 periodic boundary conditions, this requires a slower PBC
553 algorithm and molecules are not made whole in the output
555 .. mdp:: verlet-buffer-tolerance
557 (0.005) \[kJ/mol/ps\]
559 Useful only with the :mdp:`Verlet` :mdp:`cutoff-scheme`. This sets
560 the maximum allowed error for pair interactions per particle caused
561 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
562 :mdp:`nstlist` and the Verlet buffer size are fixed (for
563 performance reasons), particle pairs not in the pair list can
564 occasionally get within the cut-off distance during
565 :mdp:`nstlist` -1 steps. This causes very small jumps in the
566 energy. In a constant-temperature ensemble, these very small energy
567 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
568 estimate assumes a homogeneous particle distribution, hence the
569 errors might be slightly underestimated for multi-phase
570 systems. (See the `reference manual`_ for details). For longer
571 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
572 overestimated, because the interactions between particles are
573 ignored. Combined with cancellation of errors, the actual drift of
574 the total energy is usually one to two orders of magnitude
575 smaller. Note that the generated buffer size takes into account
576 that the |Gromacs| pair-list setup leads to a reduction in the
577 drift by a factor 10, compared to a simple particle-pair based
578 list. Without dynamics (energy minimization etc.), the buffer is 5%
579 of the cut-off. For NVE simulations the initial temperature is
580 used, unless this is zero, in which case a buffer of 10% is
581 used. For NVE simulations the tolerance usually needs to be lowered
582 to achieve proper energy conservation on the nanosecond time
583 scale. To override the automated buffer setting, use
584 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
589 Cut-off distance for the short-range neighbor list. With the
590 :mdp:`Verlet` :mdp:`cutoff-scheme`, this is by default set by the
591 :mdp:`verlet-buffer-tolerance` option and the value of
592 :mdp:`rlist` is ignored.
597 Cut-off distance for the long-range neighbor list. This parameter
598 is only relevant for a twin-range cut-off setup with switched
599 potentials. In that case a buffer region is required to account for
600 the size of charge groups. In all other cases this parameter is
601 automatically set to the longest cut-off distance.
609 .. mdp-value:: Cut-off
611 Twin range cut-offs with neighborlist cut-off :mdp:`rlist` and
612 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rcoulomb` >=
617 Classical Ewald sum electrostatics. The real-space cut-off
618 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
619 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
620 of wave vectors used in reciprocal space is controlled by
621 :mdp:`fourierspacing`. The relative accuracy of
622 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
624 NOTE: Ewald scales as O(N^3/2) and is thus extremely slow for
625 large systems. It is included mainly for reference - in most
626 cases PME will perform much better.
630 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
631 space is similar to the Ewald sum, while the reciprocal part is
632 performed with FFTs. Grid dimensions are controlled with
633 :mdp:`fourierspacing` and the interpolation order with
634 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
635 interpolation the electrostatic forces have an accuracy of
636 2-3*10^-4. Since the error from the vdw-cutoff is larger than
637 this you might try 0.15 nm. When running in parallel the
638 interpolation parallelizes better than the FFT, so try
639 decreasing grid dimensions while increasing interpolation.
641 .. mdp-value:: P3M-AD
643 Particle-Particle Particle-Mesh algorithm with analytical
644 derivative for for long range electrostatic interactions. The
645 method and code is identical to SPME, except that the influence
646 function is optimized for the grid. This gives a slight increase
649 .. mdp-value:: Reaction-Field
651 Reaction field electrostatics with Coulomb cut-off
652 :mdp:`rcoulomb`, where :mdp:`rcoulomb` >= :mdp:`rlist`. The
653 dielectric constant beyond the cut-off is
654 :mdp:`epsilon-rf`. The dielectric constant can be set to
655 infinity by setting :mdp:`epsilon-rf` =0.
657 .. mdp-value:: Generalized-Reaction-Field
659 Generalized reaction field with Coulomb cut-off
660 :mdp:`rcoulomb`, where :mdp:`rcoulomb` >= :mdp:`rlist`. The
661 dielectric constant beyond the cut-off is
662 :mdp:`epsilon-rf`. The ionic strength is computed from the
663 number of charged (*i.e.* with non zero charge) charge
664 groups. The temperature for the GRF potential is set with
667 .. mdp-value:: Reaction-Field-zero
669 In |Gromacs|, normal reaction-field electrostatics with
670 :mdp:`cutoff-scheme` = :mdp:`group` leads to bad energy
671 conservation. :mdp:`Reaction-Field-zero` solves this by making
672 the potential zero beyond the cut-off. It can only be used with
673 an infinite dielectric constant (:mdp:`epsilon-rf` =0), because
674 only for that value the force vanishes at the
675 cut-off. :mdp:`rlist` should be 0.1 to 0.3 nm larger than
676 :mdp:`rcoulomb` to accommodate for the size of charge groups
677 and diffusion between neighbor list updates. This, and the fact
678 that table lookups are used instead of analytical functions make
679 :mdp:`Reaction-Field-zero` computationally more expensive than
680 normal reaction-field.
682 .. mdp-value:: Reaction-Field-nec
684 The same as :mdp-value:`coulombtype=Reaction-Field`, but
685 implemented as in |Gromacs| versions before 3.3. No
686 reaction-field correction is applied to excluded atom pairs and
687 self pairs. The 1-4 interactions are calculated using a
688 reaction-field. The missing correction due to the excluded pairs
689 that do not have a 1-4 interaction is up to a few percent of the
690 total electrostatic energy and causes a minor difference in the
691 forces and the pressure.
695 Analogous to :mdp-value:`vdwtype=Shift` for :mdp:`vdwtype`. You
696 might want to use :mdp:`Reaction-Field-zero` instead, which has
697 a similar potential shape, but has a physical interpretation and
698 has better energies due to the exclusion correction terms.
700 .. mdp-value:: Encad-Shift
702 The Coulomb potential is decreased over the whole range, using
703 the definition from the Encad simulation package.
705 .. mdp-value:: Switch
707 Analogous to :mdp-value:`vdwtype=Switch` for
708 :mdp:`vdwtype`. Switching the Coulomb potential can lead to
709 serious artifacts, advice: use :mdp:`Reaction-Field-zero`
714 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
715 with user-defined potential functions for repulsion, dispersion
716 and Coulomb. When pair interactions are present, :ref:`gmx
717 mdrun` also expects to find a file ``tablep.xvg`` for the pair
718 interactions. When the same interactions should be used for
719 non-bonded and pair interactions the user can specify the same
720 file name for both table files. These files should contain 7
721 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
722 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
723 function, ``g(x)`` the dispersion function and ``h(x)`` the
724 repulsion function. When :mdp:`vdwtype` is not set to User the
725 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
726 the non-bonded interactions ``x`` values should run from 0 to
727 the largest cut-off distance + :mdp:`table-extension` and
728 should be uniformly spaced. For the pair interactions the table
729 length in the file will be used. The optimal spacing, which is
730 used for non-user tables, is ``0.002 nm`` when you run in mixed
731 precision or ``0.0005 nm`` when you run in double precision. The
732 function value at ``x=0`` is not important. More information is
733 in the printed manual.
735 .. mdp-value:: PME-Switch
737 A combination of PME and a switch function for the direct-space
738 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
739 :mdp:`rlist`. This is mainly useful constant energy simulations
740 (note that using PME with :mdp:`cutoff-scheme` = :mdp:`Verlet`
741 will be more efficient).
743 .. mdp-value:: PME-User
745 A combination of PME and user tables (see
746 above). :mdp:`rcoulomb` is allowed to be smaller than
747 :mdp:`rlist`. The PME mesh contribution is subtracted from the
748 user table by :ref:`gmx mdrun`. Because of this subtraction the
749 user tables should contain about 10 decimal places.
751 .. mdp-value:: PME-User-Switch
753 A combination of PME-User and a switching function (see
754 above). The switching function is applied to final
755 particle-particle interaction, *i.e.* both to the user supplied
756 function and the PME Mesh correction part.
758 .. mdp:: coulomb-modifier
760 .. mdp-value:: Potential-shift-Verlet
762 Selects Potential-shift with the Verlet cutoff-scheme, as it is
763 (nearly) free; selects None with the group cutoff-scheme.
765 .. mdp-value:: Potential-shift
767 Shift the Coulomb potential by a constant such that it is zero
768 at the cut-off. This makes the potential the integral of the
769 force. Note that this does not affect the forces or the
774 Use an unmodified Coulomb potential. With the group scheme this
775 means no exact cut-off is used, energies and forces are
776 calculated for all pairs in the neighborlist.
778 .. mdp:: rcoulomb-switch
781 where to start switching the Coulomb potential, only relevant
782 when force or potential switching is used
787 distance for the Coulomb cut-off
792 The relative dielectric constant. A value of 0 means infinity.
797 The relative dielectric constant of the reaction field. This
798 is only used with reaction-field electrostatics. A value of 0
807 .. mdp-value:: Cut-off
809 Twin range cut-offs with neighbor list cut-off :mdp:`rlist` and
810 VdW cut-off :mdp:`rvdw`, where :mdp:`rvdw` >= :mdp:`rlist`.
814 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
815 grid dimensions are controlled with :mdp:`fourierspacing` in
816 the same way as for electrostatics, and the interpolation order
817 is controlled with :mdp:`pme-order`. The relative accuracy of
818 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
819 and the specific combination rules that are to be used by the
820 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
824 This functionality is deprecated and replaced by
825 :mdp:`vdw-modifier` = Force-switch. The LJ (not Buckingham)
826 potential is decreased over the whole range and the forces decay
827 smoothly to zero between :mdp:`rvdw-switch` and
828 :mdp:`rvdw`. The neighbor search cut-off :mdp:`rlist` should
829 be 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
830 size of charge groups and diffusion between neighbor list
833 .. mdp-value:: Switch
835 This functionality is deprecated and replaced by
836 :mdp:`vdw-modifier` = Potential-switch. The LJ (not Buckingham)
837 potential is normal out to :mdp:`rvdw-switch`, after which it
838 is switched off to reach zero at :mdp:`rvdw`. Both the
839 potential and force functions are continuously smooth, but be
840 aware that all switch functions will give rise to a bulge
841 (increase) in the force (since we are switching the
842 potential). The neighbor search cut-off :mdp:`rlist` should be
843 0.1 to 0.3 nm larger than :mdp:`rvdw` to accommodate for the
844 size of charge groups and diffusion between neighbor list
847 .. mdp-value:: Encad-Shift
849 The LJ (not Buckingham) potential is decreased over the whole
850 range, using the definition from the Encad simulation package.
854 See user for :mdp:`coulombtype`. The function value at zero is
855 not important. When you want to use LJ correction, make sure
856 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
857 function. When :mdp:`coulombtype` is not set to User the values
858 for the ``f`` and ``-f'`` columns are ignored.
860 .. mdp:: vdw-modifier
862 .. mdp-value:: Potential-shift-Verlet
864 Selects Potential-shift with the Verlet cutoff-scheme, as it is
865 (nearly) free; selects None with the group cutoff-scheme.
867 .. mdp-value:: Potential-shift
869 Shift the Van der Waals potential by a constant such that it is
870 zero at the cut-off. This makes the potential the integral of
871 the force. Note that this does not affect the forces or the
876 Use an unmodified Van der Waals potential. With the group scheme
877 this means no exact cut-off is used, energies and forces are
878 calculated for all pairs in the neighborlist.
880 .. mdp-value:: Force-switch
882 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
883 and :mdp:`rvdw`. This shifts the potential shift over the whole
884 range and switches it to zero at the cut-off. Note that this is
885 more expensive to calculate than a plain cut-off and it is not
886 required for energy conservation, since Potential-shift
887 conserves energy just as well.
889 .. mdp-value:: Potential-switch
891 Smoothly switches the potential to zero between
892 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
893 articifically large forces in the switching region and is much
894 more expensive to calculate. This option should only be used if
895 the force field you are using requires this.
901 where to start switching the LJ force and possibly the potential,
902 only relevant when force or potential switching is used
907 distance for the LJ or Buckingham cut-off
913 don't apply any correction
915 .. mdp-value:: EnerPres
917 apply long range dispersion corrections for Energy and Pressure
921 apply long range dispersion corrections for Energy only
927 .. mdp:: table-extension
930 Extension of the non-bonded potential lookup tables beyond the
931 largest cut-off distance. The value should be large enough to
932 account for charge group sizes and the diffusion between
933 neighbor-list updates. Without user defined potential the same
934 table length is used for the lookup tables for the 1-4
935 interactions, which are always tabulated irrespective of the use of
936 tables for the non-bonded interactions. The value of
937 :mdp:`table-extension` in no way affects the values of
938 :mdp:`rlist`, :mdp:`rcoulomb`, or :mdp:`rvdw`.
940 .. mdp:: energygrp-table
942 When user tables are used for electrostatics and/or VdW, here one
943 can give pairs of energy groups for which seperate user tables
944 should be used. The two energy groups will be appended to the table
945 file name, in order of their definition in :mdp:`energygrps`,
946 seperated by underscores. For example, if ``energygrps = Na Cl
947 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
948 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
949 normal ``table.xvg`` which will be used for all other energy group
956 .. mdp:: fourierspacing
959 For ordinary Ewald, the ratio of the box dimensions and the spacing
960 determines a lower bound for the number of wave vectors to use in
961 each (signed) direction. For PME and P3M, that ratio determines a
962 lower bound for the number of Fourier-space grid points that will
963 be used along that axis. In all cases, the number for each
964 direction can be overridden by entering a non-zero value for that
965 :mdp:`fourier-nx` direction. For optimizing the relative load of
966 the particle-particle interactions and the mesh part of PME, it is
967 useful to know that the accuracy of the electrostatics remains
968 nearly constant when the Coulomb cut-off and the PME grid spacing
969 are scaled by the same factor.
976 Highest magnitude of wave vectors in reciprocal space when using Ewald.
977 Grid size when using PME or P3M. These values override
978 :mdp:`fourierspacing` per direction. The best choice is powers of
979 2, 3, 5 and 7. Avoid large primes.
984 Interpolation order for PME. 4 equals cubic interpolation. You
985 might try 6/8/10 when running in parallel and simultaneously
986 decrease grid dimension.
991 The relative strength of the Ewald-shifted direct potential at
992 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
993 will give a more accurate direct sum, but then you need more wave
994 vectors for the reciprocal sum.
996 .. mdp:: ewald-rtol-lj
999 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
1000 to control the relative strength of the dispersion potential at
1001 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
1002 electrostatic potential.
1004 .. mdp:: lj-pme-comb-rule
1007 The combination rules used to combine VdW-parameters in the
1008 reciprocal part of LJ-PME. Geometric rules are much faster than
1009 Lorentz-Berthelot and usually the recommended choice, even when the
1010 rest of the force field uses the Lorentz-Berthelot rules.
1012 .. mdp-value:: Geometric
1014 Apply geometric combination rules
1016 .. mdp-value:: Lorentz-Berthelot
1018 Apply Lorentz-Berthelot combination rules
1020 .. mdp:: ewald-geometry
1024 The Ewald sum is performed in all three dimensions.
1028 The reciprocal sum is still performed in 3D, but a force and
1029 potential correction applied in the `z` dimension to produce a
1030 pseudo-2D summation. If your system has a slab geometry in the
1031 `x-y` plane you can try to increase the `z`-dimension of the box
1032 (a box height of 3 times the slab height is usually ok) and use
1035 .. mdp:: epsilon-surface
1038 This controls the dipole correction to the Ewald summation in
1039 3D. The default value of zero means it is turned off. Turn it on by
1040 setting it to the value of the relative permittivity of the
1041 imaginary surface around your infinite system. Be careful - you
1042 shouldn't use this if you have free mobile charges in your
1043 system. This value does not affect the slab 3DC variant of the long
1047 Temperature coupling
1048 ^^^^^^^^^^^^^^^^^^^^
1054 No temperature coupling.
1056 .. mdp-value:: berendsen
1058 Temperature coupling with a Berendsen-thermostat to a bath with
1059 temperature :mdp:`ref-t`, with time constant
1060 :mdp:`tau-t`. Several groups can be coupled separately, these
1061 are specified in the :mdp:`tc-grps` field separated by spaces.
1063 .. mdp-value:: nose-hoover
1065 Temperature coupling using a Nose-Hoover extended ensemble. The
1066 reference temperature and coupling groups are selected as above,
1067 but in this case :mdp:`tau-t` controls the period of the
1068 temperature fluctuations at equilibrium, which is slightly
1069 different from a relaxation time. For NVT simulations the
1070 conserved energy quantity is written to energy and log file.
1072 .. mdp-value:: andersen
1074 Temperature coupling by randomizing a fraction of the particles
1075 at each timestep. Reference temperature and coupling groups are
1076 selected as above. :mdp:`tau-t` is the average time between
1077 randomization of each molecule. Inhibits particle dynamics
1078 somewhat, but little or no ergodicity issues. Currently only
1079 implemented with velocity Verlet, and not implemented with
1082 .. mdp-value:: andersen-massive
1084 Temperature coupling by randomizing all particles at infrequent
1085 timesteps. Reference temperature and coupling groups are
1086 selected as above. :mdp:`tau-t` is the time between
1087 randomization of all molecules. Inhibits particle dynamics
1088 somewhat, but little or no ergodicity issues. Currently only
1089 implemented with velocity Verlet.
1091 .. mdp-value:: v-rescale
1093 Temperature coupling using velocity rescaling with a stochastic
1094 term (JCP 126, 014101). This thermostat is similar to Berendsen
1095 coupling, with the same scaling using :mdp:`tau-t`, but the
1096 stochastic term ensures that a proper canonical ensemble is
1097 generated. The random seed is set with :mdp:`ld-seed`. This
1098 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
1099 simulations the conserved energy quantity is written to the
1100 energy and log file.
1105 The frequency for coupling the temperature. The default value of -1
1106 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
1107 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1108 Verlet integrators :mdp:`nsttcouple` is set to 1.
1110 .. mdp:: nh-chain-length
1113 The number of chained Nose-Hoover thermostats for velocity Verlet
1114 integrators, the leap-frog :mdp-value:`integrator=md` integrator
1115 only supports 1. Data for the NH chain variables is not printed to
1116 the :ref:`edr` file, but can be using the ``GMX_NOSEHOOVER_CHAINS``
1117 environment variable
1121 groups to couple to separate temperature baths
1126 time constant for coupling (one for each group in
1127 :mdp:`tc-grps`), -1 means no temperature coupling
1132 reference temperature for coupling (one for each group in
1143 No pressure coupling. This means a fixed box size.
1145 .. mdp-value:: Berendsen
1147 Exponential relaxation pressure coupling with time constant
1148 :mdp:`tau-p`. The box is scaled every timestep. It has been
1149 argued that this does not yield a correct thermodynamic
1150 ensemble, but it is the most efficient way to scale a box at the
1153 .. mdp-value:: Parrinello-Rahman
1155 Extended-ensemble pressure coupling where the box vectors are
1156 subject to an equation of motion. The equation of motion for the
1157 atoms is coupled to this. No instantaneous scaling takes
1158 place. As for Nose-Hoover temperature coupling the time constant
1159 :mdp:`tau-p` is the period of pressure fluctuations at
1160 equilibrium. This is probably a better method when you want to
1161 apply pressure scaling during data collection, but beware that
1162 you can get very large oscillations if you are starting from a
1163 different pressure. For simulations where the exact fluctation
1164 of the NPT ensemble are important, or if the pressure coupling
1165 time is very short it may not be appropriate, as the previous
1166 time step pressure is used in some steps of the |Gromacs|
1167 implementation for the current time step pressure.
1171 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1172 :mdp-value:`md-vv` or :mdp-value:`md-vv-avek`, very similar to
1173 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1174 time constant :mdp:`tau-p` is the period of pressure
1175 fluctuations at equilibrium. This is probably a better method
1176 when you want to apply pressure scaling during data collection,
1177 but beware that you can get very large oscillations if you are
1178 starting from a different pressure. Currently (as of version
1179 5.1), it only supports isotropic scaling, and only works without
1184 Specifies the kind of isotropy of the pressure coupling used. Each
1185 kind takes one or more values for :mdp:`compressibility` and
1186 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1188 .. mdp-value:: isotropic
1190 Isotropic pressure coupling with time constant
1191 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1192 :mdp:`ref-p` is required.
1194 .. mdp-value:: semiisotropic
1196 Pressure coupling which is isotropic in the ``x`` and ``y``
1197 direction, but different in the ``z`` direction. This can be
1198 useful for membrane simulations. Two values each for
1199 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1200 ``x/y`` and ``z`` directions respectively.
1202 .. mdp-value:: anisotropic
1204 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1205 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1206 respectively. When the off-diagonal compressibilities are set to
1207 zero, a rectangular box will stay rectangular. Beware that
1208 anisotropic scaling can lead to extreme deformation of the
1211 .. mdp-value:: surface-tension
1213 Surface tension coupling for surfaces parallel to the
1214 xy-plane. Uses normal pressure coupling for the `z`-direction,
1215 while the surface tension is coupled to the `x/y` dimensions of
1216 the box. The first :mdp:`ref-p` value is the reference surface
1217 tension times the number of surfaces ``bar nm``, the second
1218 value is the reference `z`-pressure ``bar``. The two
1219 :mdp:`compressibility` values are the compressibility in the
1220 `x/y` and `z` direction respectively. The value for the
1221 `z`-compressibility should be reasonably accurate since it
1222 influences the convergence of the surface-tension, it can also
1223 be set to zero to have a box with constant height.
1228 The frequency for coupling the pressure. The default value of -1
1229 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1230 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1231 Verlet integrators :mdp:`nstpcouple` is set to 1.
1236 The time constant for pressure coupling (one value for all
1239 .. mdp:: compressibility
1242 The compressibility (NOTE: this is now really in bar^-1) For water at 1
1243 atm and 300 K the compressibility is 4.5e-5 bar^-1. The number of
1244 required values is implied by :mdp:`pcoupltype`.
1249 The reference pressure for coupling. The number of required values
1250 is implied by :mdp:`pcoupltype`.
1252 .. mdp:: refcoord-scaling
1256 The reference coordinates for position restraints are not
1257 modified. Note that with this option the virial and pressure
1258 will depend on the absolute positions of the reference
1263 The reference coordinates are scaled with the scaling matrix of
1264 the pressure coupling.
1268 Scale the center of mass of the reference coordinates with the
1269 scaling matrix of the pressure coupling. The vectors of each
1270 reference coordinate to the center of mass are not scaled. Only
1271 one COM is used, even when there are multiple molecules with
1272 position restraints. For calculating the COM of the reference
1273 coordinates in the starting configuration, periodic boundary
1274 conditions are not taken into account.
1280 Simulated annealing is controlled separately for each temperature
1281 group in |Gromacs|. The reference temperature is a piecewise linear
1282 function, but you can use an arbitrary number of points for each
1283 group, and choose either a single sequence or a periodic behaviour for
1284 each group. The actual annealing is performed by dynamically changing
1285 the reference temperature used in the thermostat algorithm selected,
1286 so remember that the system will usually not instantaneously reach the
1287 reference temperature!
1291 Type of annealing for each temperature group
1295 No simulated annealing - just couple to reference temperature value.
1297 .. mdp-value:: single
1299 A single sequence of annealing points. If your simulation is
1300 longer than the time of the last point, the temperature will be
1301 coupled to this constant value after the annealing sequence has
1302 reached the last time point.
1304 .. mdp-value:: periodic
1306 The annealing will start over at the first reference point once
1307 the last reference time is reached. This is repeated until the
1310 .. mdp:: annealing-npoints
1312 A list with the number of annealing reference/control points used
1313 for each temperature group. Use 0 for groups that are not
1314 annealed. The number of entries should equal the number of
1317 .. mdp:: annealing-time
1319 List of times at the annealing reference/control points for each
1320 group. If you are using periodic annealing, the times will be used
1321 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1322 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1323 etc. The number of entries should equal the sum of the numbers
1324 given in :mdp:`annealing-npoints`.
1326 .. mdp:: annealing-temp
1328 List of temperatures at the annealing reference/control points for
1329 each group. The number of entries should equal the sum of the
1330 numbers given in :mdp:`annealing-npoints`.
1332 Confused? OK, let's use an example. Assume you have two temperature
1333 groups, set the group selections to ``annealing = single periodic``,
1334 the number of points of each group to ``annealing-npoints = 3 4``, the
1335 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1336 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1337 will be coupled to 298K at 0ps, but the reference temperature will
1338 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1339 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1340 second group is coupled to 298K at 0ps, it increases linearly to 320K
1341 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1342 decreases to 298K, and then it starts over with the same pattern
1343 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1344 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1354 Do not generate velocities. The velocities are set to zero
1355 when there are no velocities in the input structure file.
1359 Generate velocities in :ref:`gmx grompp` according to a
1360 Maxwell distribution at temperature :mdp:`gen-temp`, with
1361 random seed :mdp:`gen-seed`. This is only meaningful with
1362 integrator :mdp-value:`integrator=md`.
1367 temperature for Maxwell distribution
1372 used to initialize random generator for random velocities,
1373 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1380 .. mdp:: constraints
1384 No constraints except for those defined explicitly in the
1385 topology, *i.e.* bonds are represented by a harmonic (or other)
1386 potential or a Morse potential (depending on the setting of
1387 :mdp:`morse`) and angles by a harmonic (or other) potential.
1389 .. mdp-value:: h-bonds
1391 Convert the bonds with H-atoms to constraints.
1393 .. mdp-value:: all-bonds
1395 Convert all bonds to constraints.
1397 .. mdp-value:: h-angles
1399 Convert all bonds and additionally the angles that involve
1400 H-atoms to bond-constraints.
1402 .. mdp-value:: all-angles
1404 Convert all bonds and angles to bond-constraints.
1406 .. mdp:: constraint-algorithm
1408 .. mdp-value:: LINCS
1410 LINear Constraint Solver. With domain decomposition the parallel
1411 version P-LINCS is used. The accuracy in set with
1412 :mdp:`lincs-order`, which sets the number of matrices in the
1413 expansion for the matrix inversion. After the matrix inversion
1414 correction the algorithm does an iterative correction to
1415 compensate for lengthening due to rotation. The number of such
1416 iterations can be controlled with :mdp:`lincs-iter`. The root
1417 mean square relative constraint deviation is printed to the log
1418 file every :mdp:`nstlog` steps. If a bond rotates more than
1419 :mdp:`lincs-warnangle` in one step, a warning will be printed
1420 both to the log file and to ``stderr``. LINCS should not be used
1421 with coupled angle constraints.
1423 .. mdp-value:: SHAKE
1425 SHAKE is slightly slower and less stable than LINCS, but does
1426 work with angle constraints. The relative tolerance is set with
1427 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1428 does not support constraints between atoms on different nodes,
1429 thus it can not be used with domain decompositon when inter
1430 charge-group constraints are present. SHAKE can not be used with
1431 energy minimization.
1433 .. mdp:: continuation
1435 This option was formerly known as unconstrained-start.
1439 apply constraints to the start configuration and reset shells
1443 do not apply constraints to the start configuration and do not
1444 reset shells, useful for exact coninuation and reruns
1449 relative tolerance for SHAKE
1451 .. mdp:: lincs-order
1454 Highest order in the expansion of the constraint coupling
1455 matrix. When constraints form triangles, an additional expansion of
1456 the same order is applied on top of the normal expansion only for
1457 the couplings within such triangles. For "normal" MD simulations an
1458 order of 4 usually suffices, 6 is needed for large time-steps with
1459 virtual sites or BD. For accurate energy minimization an order of 8
1460 or more might be required. With domain decomposition, the cell size
1461 is limited by the distance spanned by :mdp:`lincs-order` +1
1462 constraints. When one wants to scale further than this limit, one
1463 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1464 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1465 )* :mdp:`lincs-order` remains constant.
1470 Number of iterations to correct for rotational lengthening in
1471 LINCS. For normal runs a single step is sufficient, but for NVE
1472 runs where you want to conserve energy accurately or for accurate
1473 energy minimization you might want to increase it to 2.
1475 .. mdp:: lincs-warnangle
1478 maximum angle that a bond can rotate before LINCS will complain
1484 bonds are represented by a harmonic potential
1488 bonds are represented by a Morse potential
1491 Energy group exclusions
1492 ^^^^^^^^^^^^^^^^^^^^^^^
1494 .. mdp:: energygrp-excl
1496 Pairs of energy groups for which all non-bonded interactions are
1497 excluded. An example: if you have two energy groups ``Protein`` and
1498 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1499 would give only the non-bonded interactions between the protein and
1500 the solvent. This is especially useful for speeding up energy
1501 calculations with ``mdrun -rerun`` and for excluding interactions
1502 within frozen groups.
1511 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1512 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1513 ``=xy``. When set to 2 pressure coupling and Ewald summation can be
1514 used (it is usually best to use semiisotropic pressure coupling
1515 with the ``x/y`` compressibility set to 0, as otherwise the surface
1516 area will change). Walls interact wit the rest of the system
1517 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1518 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1519 monitor the interaction of energy groups with each wall. The center
1520 of mass motion removal will be turned off in the ``z``-direction.
1522 .. mdp:: wall-atomtype
1524 the atom type name in the force field for each wall. By (for
1525 example) defining a special wall atom type in the topology with its
1526 own combination rules, this allows for independent tuning of the
1527 interaction of each atomtype with the walls.
1533 LJ integrated over the volume behind the wall: 9-3 potential
1537 LJ integrated over the wall surface: 10-4 potential
1541 direct LJ potential with the ``z`` distance from the wall
1545 user defined potentials indexed with the ``z`` distance from the
1546 wall, the tables are read analogously to the
1547 :mdp:`energygrp-table` option, where the first name is for a
1548 "normal" energy group and the second name is ``wall0`` or
1549 ``wall1``, only the dispersion and repulsion columns are used
1551 .. mdp:: wall-r-linpot
1554 Below this distance from the wall the potential is continued
1555 linearly and thus the force is constant. Setting this option to a
1556 postive value is especially useful for equilibration when some
1557 atoms are beyond a wall. When the value is <=0 (<0 for
1558 :mdp:`wall-type` =table), a fatal error is generated when atoms
1561 .. mdp:: wall-density
1564 the number density of the atoms for each wall for wall types 9-3
1567 .. mdp:: wall-ewald-zfac
1570 The scaling factor for the third box vector for Ewald summation
1571 only, the minimum is 2. Ewald summation can only be used with
1572 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1573 ``=3dc``. The empty layer in the box serves to decrease the
1574 unphysical Coulomb interaction between periodic images.
1580 Note that where pulling coordinate are applicable, there can be more
1581 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1582 variables will exist accordingly. Documentation references to things
1583 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1584 applicable pulling coordinate.
1590 No center of mass pulling. All the following pull options will
1591 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1596 Center of mass pulling will be applied on 1 or more groups using
1597 1 or more pull coordinates.
1599 .. mdp:: pull-cylinder-r
1602 the radius of the cylinder for
1603 :mdp:`pull-coord1-geometry` = :mdp-value:`cylinder`
1605 .. mdp:: pull-constr-tol
1608 the relative constraint tolerance for constraint pulling
1610 .. mdp:: pull-print-com1
1614 do not print the COM of the first group in each pull coordinate
1618 print the COM of the first group in each pull coordinate
1620 .. mdp:: pull-print-com2
1624 do not print the COM of the second group in each pull coordinate
1628 print the COM of the second group in each pull coordinate
1630 .. mdp:: pull-print-ref-value
1634 do not print the reference value for each pull coordinate
1638 print the reference value for each pull coordinate
1640 .. mdp:: pull-print-components
1644 only print the distance for each pull coordinate
1648 print the distance and Cartesian components selected in
1649 :mdp:`pull-coord1-dim`
1651 .. mdp:: pull-nstxout
1654 frequency for writing out the COMs of all the pull group (0 is
1657 .. mdp:: pull-nstfout
1660 frequency for writing out the force of all the pulled group
1664 .. mdp:: pull-ngroups
1667 The number of pull groups, not including the absolute reference
1668 group, when used. Pull groups can be reused in multiple pull
1669 coordinates. Below only the pull options for group 1 are given,
1670 further groups simply increase the group index number.
1672 .. mdp:: pull-ncoords
1675 The number of pull coordinates. Below only the pull options for
1676 coordinate 1 are given, further coordinates simply increase the
1677 coordinate index number.
1679 .. mdp:: pull-group1-name
1681 The name of the pull group, is looked up in the index file or in
1682 the default groups to obtain the atoms involved.
1684 .. mdp:: pull-group1-weights
1686 Optional relative weights which are multiplied with the masses of
1687 the atoms to give the total weight for the COM. The number should
1688 be 0, meaning all 1, or the number of atoms in the pull group.
1690 .. mdp:: pull-group1-pbcatom
1693 The reference atom for the treatment of periodic boundary
1694 conditions inside the group (this has no effect on the treatment of
1695 the pbc between groups). This option is only important when the
1696 diameter of the pull group is larger than half the shortest box
1697 vector. For determining the COM, all atoms in the group are put at
1698 their periodic image which is closest to
1699 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1700 atom (number wise) is used. This parameter is not used with
1701 :mdp:`pull-group1-geometry` cylinder. A value of -1 turns on cosine
1702 weighting, which is useful for a group of molecules in a periodic
1703 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1706 .. mdp:: pull-coord1-type
1708 .. mdp-value:: umbrella
1710 Center of mass pulling using an umbrella potential between the
1711 reference group and one or more groups.
1713 .. mdp-value:: constraint
1715 Center of mass pulling using a constraint between the reference
1716 group and one or more groups. The setup is identical to the
1717 option umbrella, except for the fact that a rigid constraint is
1718 applied instead of a harmonic potential.
1720 .. mdp-value:: constant-force
1722 Center of mass pulling using a linear potential and therefore a
1723 constant force. For this option there is no reference position
1724 and therefore the parameters :mdp:`pull-coord1-init` and
1725 :mdp:`pull-coord1-rate` are not used.
1727 .. mdp-value:: flat-bottom
1729 At distances beyond :mdp:`pull-coord1-init` a harmonic potential
1730 is applied, otherwise no potential is applied.
1732 .. mdp:: pull-coord1-geometry
1734 .. mdp-value:: distance
1736 Pull along the vector connecting the two groups. Components can
1737 be selected with :mdp:`pull-coord1-dim`.
1739 .. mdp-value:: direction
1741 Pull in the direction of :mdp:`pull-coord1-vec`.
1743 .. mdp-value:: direction-periodic
1745 As :mdp-value:`direction`, but allows the distance to be larger
1746 than half the box size. With this geometry the box should not be
1747 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1748 the pull force is not added to virial.
1750 .. mdp-value:: direction-relative
1752 As :mdp-value:`direction`, but the pull vector is the vector
1753 that points from the COM of a third to the COM of a fourth pull
1754 group. This means that 4 groups need to be supplied in
1755 :mdp:`pull-coord1-groups`. Note that the pull force will give
1756 rise to a torque on the pull vector, which is turn leads to
1757 forces perpendicular to the pull vector on the two groups
1758 defining the vector. If you want a pull group to move between
1759 the two groups defining the vector, simply use the union of
1760 these two groups as the reference group.
1762 .. mdp-value:: cylinder
1764 Designed for pulling with respect to a layer where the reference
1765 COM is given by a local cylindrical part of the reference group.
1766 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1767 the first of the two groups in :mdp:`pull-coord1-groups` a
1768 cylinder is selected around the axis going through the COM of
1769 the second group with direction :mdp:`pull-coord1-vec` with
1770 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1771 continously to zero as the radial distance goes from 0 to
1772 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1773 dependence gives rise to radial forces on both pull groups.
1774 Note that the radius should be smaller than half the box size.
1775 For tilted cylinders they should be even smaller than half the
1776 box size since the distance of an atom in the reference group
1777 from the COM of the pull group has both a radial and an axial
1778 component. This geometry is not supported with constraint
1781 .. mdp:: pull-coord1-groups
1783 The two groups indices should be given on which this pull
1784 coordinate will operate. The first index can be 0, in which case an
1785 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1786 absolute reference the system is no longer translation invariant
1787 and one should think about what to do with the center of mass
1788 motion. Note that (only) for :mdp:`pull-coord1-geometry` =
1789 :mdp-value:`direction-relative` four groups are required.
1791 .. mdp:: pull-coord1-dim
1794 Selects the dimensions that this pull coordinate acts on and that
1795 are printed to the output files when
1796 :mdp:`pull-print-components` = :mdp-value:`yes`. With
1797 :mdp:`pull-coord1-geometry` = :mdp-value:`distance`, only Cartesian
1798 components set to Y contribute to the distance. Thus setting this
1799 to Y Y N results in a distance in the x/y plane. With other
1800 geometries all dimensions with non-zero entries in
1801 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1802 dimensions only affect the output.
1804 .. mdp:: pull-coord1-origin
1807 The pull reference position for use with an absolute reference.
1809 .. mdp:: pull-coord1-vec
1812 The pull direction. :ref:`gmx grompp` normalizes the vector.
1814 .. mdp:: pull-coord1-start
1818 do not modify :mdp:`pull-coord1-init`
1822 add the COM distance of the starting conformation to
1823 :mdp:`pull-coord1-init`
1825 .. mdp:: pull-coord1-init
1828 The reference distance at t=0.
1830 .. mdp:: pull-coord1-rate
1833 The rate of change of the reference position.
1835 .. mdp:: pull-coord1-k
1837 (0) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\]
1838 The force constant. For umbrella pulling this is the harmonic force
1839 constant in kJ mol-1 nm-2. For constant force pulling this is the
1840 force constant of the linear potential, and thus the negative (!)
1841 of the constant force in kJ mol-1 nm-1.
1843 .. mdp:: pull-coord1-kB
1845 (pull-k1) \[kJ mol-1 nm-2\] / \[kJ mol-1 nm-1\]
1846 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1847 :mdp:`free-energy` is turned on. The force constant is then (1 -
1848 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1858 ignore distance restraint information in topology file
1860 .. mdp-value:: simple
1862 simple (per-molecule) distance restraints.
1864 .. mdp-value:: ensemble
1866 distance restraints over an ensemble of molecules in one
1867 simulation box. Normally, one would perform ensemble averaging
1868 over multiple subsystems, each in a separate box, using ``mdrun
1869 -multi``. Supply ``topol0.tpr``, ``topol1.tpr``, ... with
1870 different coordinates and/or velocities. The environment
1871 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
1872 within each ensemble (usually equal to the ``mdrun -multi``
1875 .. mdp:: disre-weighting
1877 .. mdp-value:: equal
1879 divide the restraint force equally over all atom pairs in the
1882 .. mdp-value:: conservative
1884 the forces are the derivative of the restraint potential, this
1885 results in an weighting of the atom pairs to the reciprocal
1886 seventh power of the displacement. The forces are conservative
1887 when :mdp:`disre-tau` is zero.
1889 .. mdp:: disre-mixed
1893 the violation used in the calculation of the restraint force is
1894 the time-averaged violation
1898 the violation used in the calculation of the restraint force is
1899 the square root of the product of the time-averaged violation
1900 and the instantaneous violation
1904 (1000) \[kJ mol-1 nm-2\]
1905 force constant for distance restraints, which is multiplied by a
1906 (possibly) different factor for each restraint given in the `fac`
1907 column of the interaction in the topology file.
1912 time constant for distance restraints running average. A value of
1913 zero turns off time averaging.
1915 .. mdp:: nstdisreout
1918 period between steps when the running time-averaged and
1919 instantaneous distances of all atom pairs involved in restraints
1920 are written to the energy file (can make the energy file very
1927 ignore orientation restraint information in topology file
1931 use orientation restraints, ensemble averaging can be performed
1937 force constant for orientation restraints, which is multiplied by a
1938 (possibly) different weight factor for each restraint, can be set
1939 to zero to obtain the orientations from a free simulation
1944 time constant for orientation restraints running average. A value
1945 of zero turns off time averaging.
1947 .. mdp:: orire-fitgrp
1949 fit group for orientation restraining. This group of atoms is used
1950 to determine the rotation **R** of the system with respect to the
1951 reference orientation. The reference orientation is the starting
1952 conformation of the first subsystem. For a protein, backbone is a
1955 .. mdp:: nstorireout
1958 period between steps when the running time-averaged and
1959 instantaneous orientations for all restraints, and the molecular
1960 order tensor are written to the energy file (can make the energy
1964 Free energy calculations
1965 ^^^^^^^^^^^^^^^^^^^^^^^^
1967 .. mdp:: free-energy
1971 Only use topology A.
1975 Interpolate between topology A (lambda=0) to topology B
1976 (lambda=1) and write the derivative of the Hamiltonian with
1977 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
1978 or the Hamiltonian differences with respect to other lambda
1979 values (as specified with foreign lambda) to the energy file
1980 and/or to ``dhdl.xvg``, where they can be processed by, for
1981 example :ref:`gmx bar`. The potentials, bond-lengths and angles
1982 are interpolated linearly as described in the manual. When
1983 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
1984 used for the LJ and Coulomb interactions.
1988 Turns on expanded ensemble simulation, where the alchemical state
1989 becomes a dynamic variable, allowing jumping between different
1990 Hamiltonians. See the expanded ensemble options for controlling how
1991 expanded ensemble simulations are performed. The different
1992 Hamiltonians used in expanded ensemble simulations are defined by
1993 the other free energy options.
1995 .. mdp:: init-lambda
1998 starting value for lambda (float). Generally, this should only be
1999 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2000 other cases, :mdp:`init-lambda-state` should be specified
2001 instead. Must be greater than or equal to 0.
2003 .. mdp:: delta-lambda
2006 increment per time step for lambda
2008 .. mdp:: init-lambda-state
2011 starting value for the lambda state (integer). Specifies which
2012 columm of the lambda vector (:mdp:`coul-lambdas`,
2013 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2014 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2015 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2016 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2017 the first column, and so on.
2019 .. mdp:: fep-lambdas
2022 Zero, one or more lambda values for which Delta H values will be
2023 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2024 steps. Values must be between 0 and 1. Free energy differences
2025 between different lambda values can then be determined with
2026 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2027 other -lambdas keywords because all components of the lambda vector
2028 that are not specified will use :mdp:`fep-lambdas` (including
2029 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2031 .. mdp:: coul-lambdas
2034 Zero, one or more lambda values for which Delta H values will be
2035 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2036 steps. Values must be between 0 and 1. Only the electrostatic
2037 interactions are controlled with this component of the lambda
2038 vector (and only if the lambda=0 and lambda=1 states have differing
2039 electrostatic interactions).
2041 .. mdp:: vdw-lambdas
2044 Zero, one or more lambda values for which Delta H values will be
2045 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2046 steps. Values must be between 0 and 1. Only the van der Waals
2047 interactions are controlled with this component of the lambda
2050 .. mdp:: bonded-lambdas
2053 Zero, one or more lambda values for which Delta H values will be
2054 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2055 steps. Values must be between 0 and 1. Only the bonded interactions
2056 are controlled with this component of the lambda vector.
2058 .. mdp:: restraint-lambdas
2061 Zero, one or more lambda values for which Delta H values will be
2062 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2063 steps. Values must be between 0 and 1. Only the restraint
2064 interactions: dihedral restraints, and the pull code restraints are
2065 controlled with this component of the lambda vector.
2067 .. mdp:: mass-lambdas
2070 Zero, one or more lambda values for which Delta H values will be
2071 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2072 steps. Values must be between 0 and 1. Only the particle masses are
2073 controlled with this component of the lambda vector.
2075 .. mdp:: temperature-lambdas
2078 Zero, one or more lambda values for which Delta H values will be
2079 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2080 steps. Values must be between 0 and 1. Only the temperatures
2081 controlled with this component of the lambda vector. Note that
2082 these lambdas should not be used for replica exchange, only for
2083 simulated tempering.
2085 .. mdp:: calc-lambda-neighbors
2088 Controls the number of lambda values for which Delta H values will
2089 be calculated and written out, if :mdp:`init-lambda-state` has
2090 been set. A positive value will limit the number of lambda points
2091 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2092 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2093 has a value of 2, energies for lambda points 3-7 will be calculated
2094 and writen out. A value of -1 means all lambda points will be
2095 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2096 1 is sufficient, while for MBAR -1 should be used.
2101 the soft-core alpha parameter, a value of 0 results in linear
2102 interpolation of the LJ and Coulomb interactions
2107 the power of the radial term in the soft-core equation. Possible
2108 values are 6 and 48. 6 is more standard, and is the default. When
2109 48 is used, then sc-alpha should generally be much lower (between
2115 Whether to apply the soft-core free energy interaction
2116 transformation to the Columbic interaction of a molecule. Default
2117 is no, as it is generally more efficient to turn off the Coulomic
2118 interactions linearly before turning off the van der Waals
2119 interactions. Note that it is only taken into account when lambda
2120 states are used, not with :mdp:`couple-lambda0` /
2121 :mdp:`couple-lambda1`, and you can still turn off soft-core
2122 interactions by setting :mdp:`sc-alpha` to 0.
2127 the power for lambda in the soft-core function, only the values 1
2133 the soft-core sigma for particles which have a C6 or C12 parameter
2134 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2136 .. mdp:: couple-moltype
2138 Here one can supply a molecule type (as defined in the topology)
2139 for calculating solvation or coupling free energies. There is a
2140 special option ``system`` that couples all molecule types in the
2141 system. This can be useful for equilibrating a system starting from
2142 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2143 on. The Van der Waals interactions and/or charges in this molecule
2144 type can be turned on or off between lambda=0 and lambda=1,
2145 depending on the settings of :mdp:`couple-lambda0` and
2146 :mdp:`couple-lambda1`. If you want to decouple one of several
2147 copies of a molecule, you need to copy and rename the molecule
2148 definition in the topology.
2150 .. mdp:: couple-lambda0
2152 .. mdp-value:: vdw-q
2154 all interactions are on at lambda=0
2158 the charges are zero (no Coulomb interactions) at lambda=0
2162 the Van der Waals interactions are turned at lambda=0; soft-core
2163 interactions will be required to avoid singularities
2167 the Van der Waals interactions are turned off and the charges
2168 are zero at lambda=0; soft-core interactions will be required to
2169 avoid singularities.
2171 .. mdp:: couple-lambda1
2173 analogous to :mdp:`couple-lambda1`, but for lambda=1
2175 .. mdp:: couple-intramol
2179 All intra-molecular non-bonded interactions for moleculetype
2180 :mdp:`couple-moltype` are replaced by exclusions and explicit
2181 pair interactions. In this manner the decoupled state of the
2182 molecule corresponds to the proper vacuum state without
2183 periodicity effects.
2187 The intra-molecular Van der Waals and Coulomb interactions are
2188 also turned on/off. This can be useful for partitioning
2189 free-energies of relatively large molecules, where the
2190 intra-molecular non-bonded interactions might lead to
2191 kinetically trapped vacuum conformations. The 1-4 pair
2192 interactions are not turned off.
2197 the frequency for writing dH/dlambda and possibly Delta H to
2198 dhdl.xvg, 0 means no ouput, should be a multiple of
2199 :mdp:`nstcalcenergy`.
2201 .. mdp:: dhdl-derivatives
2205 If yes (the default), the derivatives of the Hamiltonian with
2206 respect to lambda at each :mdp:`nstdhdl` step are written
2207 out. These values are needed for interpolation of linear energy
2208 differences with :ref:`gmx bar` (although the same can also be
2209 achieved with the right foreign lambda setting, that may not be as
2210 flexible), or with thermodynamic integration
2212 .. mdp:: dhdl-print-energy
2216 Include either the total or the potential energy in the dhdl
2217 file. Options are 'no', 'potential', or 'total'. This information
2218 is needed for later free energy analysis if the states of interest
2219 are at different temperatures. If all states are at the same
2220 temperature, this information is not needed. 'potential' is useful
2221 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2222 file. When rerunning from an existing trajectory, the kinetic
2223 energy will often not be correct, and thus one must compute the
2224 residual free energy from the potential alone, with the kinetic
2225 energy component computed analytically.
2227 .. mdp:: separate-dhdl-file
2231 The free energy values that are calculated (as specified with
2232 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2233 written out to a separate file, with the default name
2234 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2239 The free energy values are written out to the energy output file
2240 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2241 steps), where they can be extracted with :ref:`gmx energy` or
2242 used directly with :ref:`gmx bar`.
2244 .. mdp:: dh-hist-size
2247 If nonzero, specifies the size of the histogram into which the
2248 Delta H values (specified with foreign lambda) and the derivative
2249 dH/dl values are binned, and written to ener.edr. This can be used
2250 to save disk space while calculating free energy differences. One
2251 histogram gets written for each foreign lambda and two for the
2252 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2253 histogram settings (too small size or too wide bins) can introduce
2254 errors. Do not use histograms unless you're certain you need it.
2256 .. mdp:: dh-hist-spacing
2259 Specifies the bin width of the histograms, in energy units. Used in
2260 conjunction with :mdp:`dh-hist-size`. This size limits the
2261 accuracy with which free energies can be calculated. Do not use
2262 histograms unless you're certain you need it.
2265 Expanded Ensemble calculations
2266 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2268 .. mdp:: nstexpanded
2270 The number of integration steps beween attempted moves changing the
2271 system Hamiltonian in expanded ensemble simulations. Must be a
2272 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2279 No Monte Carlo in state space is performed.
2281 .. mdp-value:: metropolis-transition
2283 Uses the Metropolis weights to update the expanded ensemble
2284 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2287 .. mdp-value:: barker-transition
2289 Uses the Barker transition critera to update the expanded
2290 ensemble weight of each state i, defined by exp(-beta_new
2291 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2293 .. mdp-value:: wang-landau
2295 Uses the Wang-Landau algorithm (in state space, not energy
2296 space) to update the expanded ensemble weights.
2298 .. mdp-value:: min-variance
2300 Uses the minimum variance updating method of Escobedo et al. to
2301 update the expanded ensemble weights. Weights will not be the
2302 free energies, but will rather emphasize states that need more
2303 sampling to give even uncertainty.
2305 .. mdp:: lmc-mc-move
2309 No Monte Carlo in state space is performed.
2311 .. mdp-value:: metropolis-transition
2313 Randomly chooses a new state up or down, then uses the
2314 Metropolis critera to decide whether to accept or reject:
2315 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2317 .. mdp-value:: barker-transition
2319 Randomly chooses a new state up or down, then uses the Barker
2320 transition critera to decide whether to accept or reject:
2321 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2323 .. mdp-value:: gibbs
2325 Uses the conditional weights of the state given the coordinate
2326 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2329 .. mdp-value:: metropolized-gibbs
2331 Uses the conditional weights of the state given the coordinate
2332 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2333 to move to, EXCLUDING the current state, then uses a rejection
2334 step to ensure detailed balance. Always more efficient that
2335 Gibbs, though only marginally so in many situations, such as
2336 when only the nearest neighbors have decent phase space
2342 random seed to use for Monte Carlo moves in state space. When
2343 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2345 .. mdp:: mc-temperature
2347 Temperature used for acceptance/rejection for Monte Carlo moves. If
2348 not specified, the temperature of the simulation specified in the
2349 first group of :mdp:`ref-t` is used.
2354 The cutoff for the histogram of state occupancies to be reset, and
2355 the free energy incrementor to be changed from delta to delta *
2356 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2357 each histogram) / (average number of samples at each
2358 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2359 histogram is only considered flat if all Nratio > 0.8 AND
2360 simultaneously all 1/Nratio > 0.8.
2365 Each time the histogram is considered flat, then the current value
2366 of the Wang-Landau incrementor for the free energies is multiplied
2367 by :mdp:`wl-scale`. Value must be between 0 and 1.
2369 .. mdp:: init-wl-delta
2372 The initial value of the Wang-Landau incrementor in kT. Some value
2373 near 1 kT is usually most efficient, though sometimes a value of
2374 2-3 in units of kT works better if the free energy differences are
2377 .. mdp:: wl-oneovert
2380 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2381 the large sample limit. There is significant evidence that the
2382 standard Wang-Landau algorithms in state space presented here
2383 result in free energies getting 'burned in' to incorrect values
2384 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2385 then when the incrementor becomes less than 1/N, where N is the
2386 mumber of samples collected (and thus proportional to the data
2387 collection time, hence '1 over t'), then the Wang-Lambda
2388 incrementor is set to 1/N, decreasing every step. Once this occurs,
2389 :mdp:`wl-ratio` is ignored, but the weights will still stop
2390 updating when the equilibration criteria set in
2391 :mdp:`lmc-weights-equil` is achieved.
2393 .. mdp:: lmc-repeats
2396 Controls the number of times that each Monte Carlo swap type is
2397 performed each iteration. In the limit of large numbers of Monte
2398 Carlo repeats, then all methods converge to Gibbs sampling. The
2399 value will generally not need to be different from 1.
2401 .. mdp:: lmc-gibbsdelta
2404 Limit Gibbs sampling to selected numbers of neighboring states. For
2405 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2406 sampling over all of the states that are defined. A positive value
2407 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2408 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2409 value of -1 means that all states are considered. For less than 100
2410 states, it is probably not that expensive to include all states.
2412 .. mdp:: lmc-forced-nstart
2415 Force initial state space sampling to generate weights. In order to
2416 come up with reasonable initial weights, this setting allows the
2417 simulation to drive from the initial to the final lambda state,
2418 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2419 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2420 sufficiently long (thousands of steps, perhaps), then the weights
2421 will be close to correct. However, in most cases, it is probably
2422 better to simply run the standard weight equilibration algorithms.
2424 .. mdp:: nst-transition-matrix
2427 Frequency of outputting the expanded ensemble transition matrix. A
2428 negative number means it will only be printed at the end of the
2431 .. mdp:: symmetrized-transition-matrix
2434 Whether to symmetrize the empirical transition matrix. In the
2435 infinite limit the matrix will be symmetric, but will diverge with
2436 statistical noise for short timescales. Forced symmetrization, by
2437 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2438 like the existence of (small magnitude) negative eigenvalues.
2440 .. mdp:: mininum-var-min
2443 The min-variance strategy (option of :mdp:`lmc-stats` is only
2444 valid for larger number of samples, and can get stuck if too few
2445 samples are used at each state. :mdp:`mininum-var-min` is the
2446 minimum number of samples that each state that are allowed before
2447 the min-variance strategy is activated if selected.
2449 .. mdp:: init-lambda-weights
2451 The initial weights (free energies) used for the expanded ensemble
2452 states. Default is a vector of zero weights. format is similar to
2453 the lambda vector settings in :mdp:`fep-lambdas`, except the
2454 weights can be any floating point number. Units are kT. Its length
2455 must match the lambda vector lengths.
2457 .. mdp:: lmc-weights-equil
2461 Expanded ensemble weights continue to be updated throughout the
2466 The input expanded ensemble weights are treated as equilibrated,
2467 and are not updated throughout the simulation.
2469 .. mdp-value:: wl-delta
2471 Expanded ensemble weight updating is stopped when the
2472 Wang-Landau incrementor falls below this value.
2474 .. mdp-value:: number-all-lambda
2476 Expanded ensemble weight updating is stopped when the number of
2477 samples at all of the lambda states is greater than this value.
2479 .. mdp-value:: number-steps
2481 Expanded ensemble weight updating is stopped when the number of
2482 steps is greater than the level specified by this value.
2484 .. mdp-value:: number-samples
2486 Expanded ensemble weight updating is stopped when the number of
2487 total samples across all lambda states is greater than the level
2488 specified by this value.
2490 .. mdp-value:: count-ratio
2492 Expanded ensemble weight updating is stopped when the ratio of
2493 samples at the least sampled lambda state and most sampled
2494 lambda state greater than this value.
2496 .. mdp:: simulated-tempering
2499 Turn simulated tempering on or off. Simulated tempering is
2500 implemented as expanded ensemble sampling with different
2501 temperatures instead of different Hamiltonians.
2503 .. mdp:: sim-temp-low
2506 Low temperature for simulated tempering.
2508 .. mdp:: sim-temp-high
2511 High temperature for simulated tempering.
2513 .. mdp:: simulated-tempering-scaling
2515 Controls the way that the temperatures at intermediate lambdas are
2516 calculated from the :mdp:`temperature-lambdas` part of the lambda
2519 .. mdp-value:: linear
2521 Linearly interpolates the temperatures using the values of
2522 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2523 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2524 a temperature of 350. A nonlinear set of temperatures can always
2525 be implemented with uneven spacing in lambda.
2527 .. mdp-value:: geometric
2529 Interpolates temperatures geometrically between
2530 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2531 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2532 :mdp:`sim-temp-low`) raised to the power of
2533 (i/(ntemps-1)). This should give roughly equal exchange for
2534 constant heat capacity, though of course things simulations that
2535 involve protein folding have very high heat capacity peaks.
2537 .. mdp-value:: exponential
2539 Interpolates temperatures exponentially between
2540 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2541 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2542 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2543 (i))-1)/(exp(1.0)-i)).
2551 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2552 in groups Protein and Sol will experience constant acceleration as
2553 specified in the :mdp:`accelerate` line
2558 acceleration for :mdp:`acc-grps`; x, y and z for each group
2559 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2560 constant acceleration of 0.1 nm ps-2 in X direction, second group
2565 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2566 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2567 specifies for which dimension the freezing applies. To avoid
2568 spurious contibrutions to the virial and pressure due to large
2569 forces between completely frozen atoms you need to use energy group
2570 exclusions, this also saves computing time. Note that coordinates
2571 of frozen atoms are not scaled by pressure-coupling algorithms.
2575 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2576 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
2577 N N N N`` means that particles in the first group can move only in
2578 Z direction. The particles in the second group can move in any
2581 .. mdp:: cos-acceleration
2584 the amplitude of the acceleration profile for calculating the
2585 viscosity. The acceleration is in the X-direction and the magnitude
2586 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2587 added to the energy file: the amplitude of the velocity profile and
2592 (0 0 0 0 0 0) \[nm ps-1\]
2593 The velocities of deformation for the box elements: a(x) b(y) c(z)
2594 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2595 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2596 elements are corrected for periodicity. The coordinates are
2597 transformed accordingly. Frozen degrees of freedom are (purposely)
2598 also transformed. The time ts is set to t at the first step and at
2599 steps at which x and v are written to trajectory to ensure exact
2600 restarts. Deformation can be used together with semiisotropic or
2601 anisotropic pressure coupling when the appropriate
2602 compressibilities are set to zero. The diagonal elements can be
2603 used to strain a solid. The off-diagonal elements can be used to
2604 shear a solid or a liquid.
2610 .. mdp:: E-x ; E-y ; E-z
2612 If you want to use an electric field in a direction, enter 3
2613 numbers after the appropriate E-direction, the first number: the
2614 number of cosines, only 1 is implemented (with frequency 0) so
2615 enter 1, the second number: the strength of the electric field in V
2616 nm^-1, the third number: the phase of the cosine, you can enter any
2617 number here since a cosine of frequency zero has no phase.
2619 .. mdp:: E-xt; E-yt; E-zt
2621 Here you can specify a pulsed alternating electric field. The field
2622 has the form of a gaussian laser pulse:
2624 E(t) = E0 exp ( -(t-t0)^2/(2 sigma^2) ) cos(omega (t-t0))
2626 For example, the four parameters for direction x are set in the
2627 three fields of :mdp:`E-x` and :mdp:`E-xt` like
2631 E-xt = omega t0 sigma
2633 In the special case that sigma = 0, the exponential term is omitted
2634 and only the cosine term is used.
2636 More details in Carl Caleman and David van der Spoel: Picosecond
2637 Melting of Ice by an Infrared Laser Pulse - A Simulation Study
2638 Angew. Chem. Intl. Ed. 47 pp. 14 17-1420 (2008)
2642 Mixed quantum/classical molecular dynamics
2643 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2653 Do a QM/MM simulation. Several groups can be described at
2654 different QM levels separately. These are specified in the
2655 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
2656 initio* theory at which the groups are described is specified by
2657 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
2658 groups at different levels of theory is only possible with the
2659 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
2663 groups to be descibed at the QM level
2667 .. mdp-value:: normal
2669 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
2670 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
2671 *ab initio* theory. The rest of the system is described at the
2672 MM level. The QM and MM subsystems interact as follows: MM point
2673 charges are included in the QM one-electron hamiltonian and all
2674 Lennard-Jones interactions are described at the MM level.
2676 .. mdp-value:: ONIOM
2678 The interaction between the subsystem is described using the
2679 ONIOM method by Morokuma and co-workers. There can be more than
2680 one :mdp:`QMMM-grps` each modeled at a different level of QM
2681 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
2686 Method used to compute the energy and gradients on the QM
2687 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
2688 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
2689 included in the active space is specified by :mdp:`CASelectrons`
2690 and :mdp:`CASorbitals`.
2695 Basis set used to expand the electronic wavefuntion. Only Gaussian
2696 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
2697 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
2702 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
2703 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
2704 layer needs to be specified separately.
2709 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
2710 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
2711 needs to be specified separately.
2713 .. mdp:: CASorbitals
2716 The number of orbitals to be included in the active space when
2717 doing a CASSCF computation.
2719 .. mdp:: CASelectrons
2722 The number of electrons to be included in the active space when
2723 doing a CASSCF computation.
2729 No surface hopping. The system is always in the electronic
2734 Do a QM/MM MD simulation on the excited state-potential energy
2735 surface and enforce a *diabatic* hop to the ground-state when
2736 the system hits the conical intersection hyperline in the course
2737 the simulation. This option only works in combination with the
2744 .. mdp:: implicit-solvent
2752 Do a simulation with implicit solvent using the Generalized Born
2753 formalism. Three different methods for calculating the Born
2754 radii are available, Still, HCT and OBC. These are specified
2755 with the :mdp:`gb-algorithm` field. The non-polar solvation is
2756 specified with the :mdp:`sa-algorithm` field.
2758 .. mdp:: gb-algorithm
2760 .. mdp-value:: Still
2762 Use the Still method to calculate the Born radii
2766 Use the Hawkins-Cramer-Truhlar method to calculate the Born
2771 Use the Onufriev-Bashford-Case method to calculate the Born
2777 Frequency to (re)-calculate the Born radii. For most practial
2778 purposes, setting a value larger than 1 violates energy
2779 conservation and leads to unstable trajectories.
2784 Cut-off for the calculation of the Born radii. Currently must be
2787 .. mdp:: gb-epsilon-solvent
2790 Dielectric constant for the implicit solvent
2792 .. mdp:: gb-saltconc
2795 Salt concentration for implicit solvent models, currently not used
2797 .. mdp:: gb-obc-alpha
2798 .. mdp:: gb-obc-beta
2799 .. mdp:: gb-obc-gamma
2801 Scale factors for the OBC model. Default values of 1, 0.78 and 4.85
2802 respectively are for OBC(II). Values for OBC(I) are 0.8, 0 and 2.91
2805 .. mdp:: gb-dielectric-offset
2808 Distance for the di-electric offset when calculating the Born
2809 radii. This is the offset between the center of each atom the
2810 center of the polarization energy for the corresponding atom
2812 .. mdp:: sa-algorithm
2814 .. mdp-value:: Ace-approximation
2816 Use an Ace-type approximation
2820 No non-polar solvation calculation done. For GBSA only the polar
2821 part gets calculated
2823 .. mdp:: sa-surface-tension
2826 Default value for surface tension with SA algorithms. The default
2827 value is -1; Note that if this default value is not changed it will
2828 be overridden by :ref:`gmx grompp` using values that are specific
2829 for the choice of radii algorithm (0.0049 kcal/mol/Angstrom^2 for
2830 Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will
2831 while using an sa-algorithm other than None means no non-polar
2832 calculations are done.
2835 Adaptive Resolution Simulation
2836 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2841 Decide whether the AdResS feature is turned on.
2843 .. mdp:: adress-type
2847 Do an AdResS simulation with weight equal 1, which is equivalent
2848 to an explicit (normal) MD simulation. The difference to
2849 disabled AdResS is that the AdResS variables are still read-in
2850 and hence are defined.
2852 .. mdp-value:: Constant
2854 Do an AdResS simulation with a constant weight,
2855 :mdp:`adress-const-wf` defines the value of the weight
2857 .. mdp-value:: XSplit
2859 Do an AdResS simulation with simulation box split in
2860 x-direction, so basically the weight is only a function of the x
2861 coordinate and all distances are measured using the x coordinate
2864 .. mdp-value:: Sphere
2866 Do an AdResS simulation with spherical explicit zone.
2868 .. mdp:: adress-const-wf
2871 Provides the weight for a constant weight simulation
2872 (:mdp:`adress-type` =Constant)
2874 .. mdp:: adress-ex-width
2877 Width of the explicit zone, measured from
2878 :mdp:`adress-reference-coords`.
2880 .. mdp:: adress-hy-width
2883 Width of the hybrid zone.
2885 .. mdp:: adress-reference-coords
2888 Position of the center of the explicit zone. Periodic boundary
2889 conditions apply for measuring the distance from it.
2891 .. mdp:: adress-cg-grp-names
2893 The names of the coarse-grained energy groups. All other energy
2894 groups are considered explicit and their interactions will be
2895 automatically excluded with the coarse-grained groups.
2897 .. mdp:: adress-site
2899 The mapping point from which the weight is calculated.
2903 The weight is calculated from the center of mass of each charge group.
2907 The weight is calculated from the center of geometry of each charge group.
2911 The weight is calculated from the position of 1st atom of each charge group.
2913 .. mdp-value:: AtomPerAtom
2915 The weight is calculated from the position of each individual atom.
2917 .. mdp:: adress-interface-correction
2921 Do not apply any interface correction.
2923 .. mdp-value:: thermoforce
2925 Apply thermodynamic force interface correction. The table can be
2926 specified using the ``-tabletf`` option of :ref:`gmx mdrun`. The
2927 table should contain the potential and force (acting on
2928 molecules) as function of the distance from
2929 :mdp:`adress-reference-coords`.
2931 .. mdp:: adress-tf-grp-names
2933 The names of the energy groups to which the thermoforce is applied
2934 if enabled in :mdp:`adress-interface-correction`. If no group is
2935 given the default table is applied.
2937 .. mdp:: adress-ex-forcecap
2940 Cap the force in the hybrid region, useful for big molecules. 0
2941 disables force capping.
2944 User defined thingies
2945 ^^^^^^^^^^^^^^^^^^^^^
2949 .. mdp:: userint1 (0)
2950 .. mdp:: userint2 (0)
2951 .. mdp:: userint3 (0)
2952 .. mdp:: userint4 (0)
2953 .. mdp:: userreal1 (0)
2954 .. mdp:: userreal2 (0)
2955 .. mdp:: userreal3 (0)
2956 .. mdp:: userreal4 (0)
2958 These you can use if you modify code. You can pass integers and
2959 reals and groups to your subroutine. Check the inputrec definition
2960 in ``src/gromacs/legacyheaders/types/inputrec.h``
2962 .. _reference manual: gmx-manual-parent-dir_