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11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdp options</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
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28 <ul>
30 <p> </p>
32 <li><A HREF="#run"><b>run control</b></A> (integrator, tinit, dt, nsteps, init-step, comm-mode, nstcomm, comm-grps)
37 <li><A HREF="#out"><b>output control</b></A> (nstxout, nstvout, nstfout, nstlog, nstcalcenergy, nstenergy, nstxtcout, xtc-precision, xtc-grps, energygrps)
38 <li><A HREF="#nl"><b>neighbor searching</b></A> (cutoff-scheme, nstlist, ns-type, pbc, periodic-molecules, verlet-buffer-drift, rlist, rlistlong)
39 <li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
42 <li><A HREF="#ewald"><b>Ewald</b></A> (fourierspacing, fourier-nx, fourier-ny, fourier-nz, pme-order, ewald-rtol, ewald-geometry, epsilon-surface, optimize-fft)
45 nstpcouple, tau-p, compressibility, ref-p, refcoord-scaling)
46 <li><A HREF="#sa"><b>simulated annealing</b></A> (annealing, annealing-npoints, annealing-time, annealing-temp)
48 <li><A HREF="#bond"><b>bonds</b></A> (constraints, constraint-algorithm, continuation, shake-tol, lincs-order, lincs-iter, lincs-warnangle, morse)
51 wall-density, wall-ewald-zfac)
53 <li><A HREF="#nmr"><b>NMR refinement</b></A> (disre, disre-weighting, disre-mixed, disre-fc, disre-tau, nstdisreout, orire, orire-fc, orire-tau, orire-fitgrp, nstorireout)
54 <li><A HREF="#free"><b>Free energy calculations</b></A> (free-energy, nstfep, nstdgdl, dhdl-print-energy, init-lambda, delta-lambda, fep-lambdas, coul-lambdas, vdw-lambdas, bonded-lambdas, restraint-lambdas, mass-lambdas, sc-alpha, sc-coul, sc-power, sc-r-power, sc-sigma, couple-moltype, couple-lambda0, couple-lambda1, couple-intramol)
55 <li><A HREF="#expanded"><b>Expanded ensemble simulation</b></A> (lmc-stats, lmc-mc-move, lmc-seed, lmc-gibbsdelta, mc-temperature, nst-transition-matrix,init-lambda-weights,initial-wl-delta,wl-scale,wl-ratio,symmetrized-transition-matrix,lmc-forced-nstart,weight-c-range,mininum-var-min,lmc-weights-equil,weight-equil-wl-delta,weight-equil-number-all-lambda,weight-equil-number-steps,weight-equil-number-samples,weight-equil-count-ratio,simulated-tempering,simulated-tempering-scaling,sim-temp-low,sim-temp-high)
56 <li><A HREF="#neq"><b>Non-equilibrium MD</b></A> (acc-grps, accelerate, freezegrps, freezedim, cos-acceleration, deform)
58 <li><A HREF="#qmmm"><b>Mixed quantum/classical dynamics</b></A> (QMMM, QMMM-grps, QMMMscheme, QMmethod, QMbasis, QMcharge, Qmmult, CASorbitals, CASelectrons, SH)
59 <li><A HREF="#gbsa"><b>Implicit solvent</b></A> (implicit-solvent, gb-algorithm, nstgbradii, rgbradii, gb-epsilon-solvent, gb-saltconc, gb-obc-alpha, gb-obc-beta, gb-obc-gamma, gb-dielectric-offset, sa-algorithm, sa-surface-tension)
60 <li><A HREF="#adress"><b>AdResS settings</b></A> (adress, adress_type, adress_const_wf, adress_ex_width, adress_hy_width, adress_ex_forcecap, adress_interface_correction, adress_site, adress_reference_coords, adress_tf_grp_names, adress_cg_grp_names)
61 <li><A HREF="#user"><b>User defined thingies</b></A> (user1-grps, user2-grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
63 </ul>
64 </P>
66 <HR>
71 <P>
72 Default values are given in parentheses. The first option in
73 the list is always the default option. Units are given in
74 square brackets The difference between a dash and an underscore
75 is ignored. </P>
77 <P>
79 available. This should be appropriate to start a normal
80 simulation. Edit it to suit your specific needs and desires. </P>
83 <hr>
86 <dl>
88 <dd>directories to include in your topology. Format:
91 <dd>defines to pass to the preprocessor, default is no defines. You can use
92 any defines to control options in your customized topology files. Options
93 that are already available by default are:
97 topology, this can be useful for normal mode analysis.</dd>
101 </dl>
102 </dl>
105 <hr>
108 <dl>
109 <dt><b>integrator:</b> (Despite the name, this list includes algorithms that are not actually integrators. <tt>steep</tt> and all entries following it are in this category)</dt>
113 for integrating Newton's equations of motion.</dd>
115 <dd>A velocity Verlet algorithm for integrating Newton's equations of motion.
116 For constant NVE simulations started from corresponding points in the same trajectory, the trajectories
117 are analytically, but not binary, identical to the <b>md</b> leap-frog integrator. The the kinetic
118 energy, which is determined from the whole step velocities and is therefore
119 slightly too high. The advantage of this integrator is more accurate,
120 reversible Nose-Hoover and Parrinello-Rahman coupling integration
121 based on Trotter expansion, as well as (slightly too small) full step velocity
122 output. This all comes at the cost off extra computation, especially with
123 constraints and extra communication in parallel. Note that for nearly all
125 </dd>
128 the kinetic energy is determined as the average of
130 With Nose-Hoover and/or Parrinello-Rahman coupling this comes with
131 a slight increase in computational cost.
132 </dd>
134 <dd> An accurate leap-frog stochastic dynamics integrator.
135 Four Gaussian random number are required
136 per integration step per degree of freedom. With constraints,
137 coordinates needs to be constrained twice per integration step.
138 Depending on the computational cost of the force calculation,
139 this can take a significant part of the simulation time.
140 The temperature for one or more groups of atoms
143 the inverse friction constant for each group is set with
148 since this results in a friction that is lower than the internal friction
149 of water, while it is high enough to remove excess heat
151 NOTE: temperature deviations decay twice as fast as with
154 <dd> An efficient leap-frog stochastic dynamics integrator.
156 only one Gaussian random number and one constraint step and is therefore
159 will often be preferred.</dd>
161 <dd>An Euler integrator for Brownian or position Langevin dynamics, the
162 velocity is the force divided by a friction coefficient
179 is done every once in a while, this is determined by
181 For a minimization prior to a normal mode analysis, which requires
182 a very high accuracy, GROMACS should be compiled in double precision.</dd>
185 according to the low-memory Broyden-Fletcher-Goldfarb-Shanno approach.
186 In practice this seems to converge faster than Conjugate Gradients, but due
187 to the correction steps necessary it is not (yet) parallelized.
188 </dd>
192 compiled in double precision.</dd>
194 <dd> Test particle insertion. The last molecule in the topology
195 is the test particle. A trajectory should be provided with
197 should not contain the molecule to be inserted. Insertions
202 around a the same random location using the same neighborlist
204 which is only allowed for single-atom molecules).
205 Since neighborlist construction is expensive, one can perform several
206 extra insertions with the same list almost for free.
208 The temperature for the Boltzmann weighting is set with
210 of the simulation of the original trajectory.
211 Dispersion correction is implemented correctly for tpi.
212 All relevant quantities are written to the file specified with
214 The distribution of insertion energies is written to the file specified with
216 No trajectory or energy file is written.
217 Parallel tpi gives identical results to single node tpi.
218 For charged molecules, using PME with a fine grid is most accurate
219 and also efficient, since the potential in the system only needs
220 to be calculated once per frame.
221 </dd>
223 <dd> Test particle insertion into a predefined cavity location.
225 extra is read from the trajectory, which is used as the insertion location.
227 not do this for you, since for different situations a different
228 way of centering might be optimal.
230 around this location. Neighbor searching is done only once per frame,
232 Parallel tpic gives identical results to single node tpic.
233 </dl>
244 <dd>The starting step.
245 The time at an step i in a run is calculated as: t = <tt>tinit</tt> + <tt>dt</tt>*(<tt>init-step</tt> + i).
246 The free-energy lambda is calculated as: lambda = <tt>init-lambda</tt> + <tt>delta-lambda</tt>*(<tt>init-step</tt> + i).
247 Also non-equilibrium MD parameters can depend on the step number.
248 Thus for exact restarts or redoing part of a run it might be necessary to
251 </dd>
257 <dd>Remove center of mass translation and rotation around the center of mass
258 </dd>
260 <dd>No restriction on the center of mass motion
261 </dl></dd>
266 </dl>
269 <hr>
272 <dl>
274 <dd>Brownian dynamics friction coefficient.
278 <dd>used to initialize random generator for thermal noise
279 for stochastic and Brownian dynamics.
281 When running BD or SD on multiple processors, each processor uses a seed equal
283 </dl>
286 <hr>
288 <dl>
290 <dd>the minimization is converged when the maximum force is smaller than
291 this value</dd>
296 conjugate gradient energy minimization.</dd>
298 <dd>Number of correction steps to use for L-BFGS minimization. A higher
299 number is (at least theoretically) more accurate, but slower.</dd>
300 </dl>
303 <hr>
305 When shells or
306 flexible constraints are present in the system the positions of the shells
307 and the lengths of the flexible constraints are optimized at
308 every time step until either the RMS force on the shells and constraints
309 is less than emtol, or a maximum number of iterations (niter) has been reached
310 <dl>
312 <dd>the minimization is converged when the maximum force is smaller than
313 this value. For shell MD this value should be 1.0 at most, but since the
316 <dd>maximum number of iterations for optimizing the shell positions
317 and the flexible constraints.</dd>
319 <dd>the step size for optimizing the flexible constraints.
321 where mu is the reduced mass of two particles in a flexible constraint
323 in the constraint direction. Hopefully this number does not differ too
324 much between the flexible constraints, as the number of iterations
326 Try several values!</dd>
327 </dl>
330 <hr>
332 <dl>
334 <dd>the test particle insertion radius see integrators
336 </dl>
339 <hr>
341 <dl>
343 <dd>frequency to write coordinates to output
346 <dd>frequency to write velocities to output trajectory,
347 the last velocities are always written</dd>
352 the last energies are always written</dd>
355 This option is only relevant with dynamics.
358 This option affects the performance in parallel simulations,
359 because calculating energies requires global communication between all
360 processes which can become a bottleneck at high parallelization.
361 </dd>
363 <dd>frequency to write energies to energy file,
364 the last energies are always written,
366 Note that the exact sums and fluctuations over all MD steps
375 <dd>group(s) to write to xtc trajectory, default the whole system is written
379 </dl>
382 <hr>
384 <dl>
388 <dd>Generate a pair list for groups of atoms. These groups correspond to the
389 charge groups in the topology. This was the only cut-off treatment scheme
390 before version 4.6.
391 There is no explicit buffering of the pair list. This enables efficient force
392 calculations, but energy is only conserved when a buffer is explicitly added.
394 and efficient algorithm.</dd>
397 <dd>Generate a pair list with buffering. The buffer size is automatically set
408 <b>Verlet<\b> is somewhat faster than <b>group</b> when there is no water, or if <b>group</b> would use a pair-list buffer to conserve energy.
409 </dd>
410 </dl></dd>
416 the long-range forces, when using twin-range cut-offs). When this is 0,
417 the neighbor list is made only once.
418 With energy minimization the neighborlist will be updated for every
420 With non-bonded force calculation on the GPU, a value of 20 or more gives
421 the best performance.</dd>
423 <dd>The neighbor list is only constructed once and never updated.
424 This is mainly useful for vacuum simulations in which all particles
425 see each other.</dd>
428 This can only be used with switched, shifted or user potentials where
431 The neighbor list is only updated when one or more particles have moved further
432 than half the buffer size from the center of geometry of their charge group
433 as determined at the previous neighbor search.
435 is taken into account.
436 This option guarantees that their are no cut-off artifacts,
437 but for larger systems this can come at a high computational cost,
438 since the neighbor list update frequency will be determined
439 by just one or two particles moving slightly beyond the half buffer length
440 (which does not necessarily imply that the neighbor list is invalid),
441 while 99.99% of the particles are fine.
442 </dd>
443 </dl></dd>
448 <dd>Make a grid in the box and only check atoms in neighboring grid
450 In large systems grid search is much faster than simple search.</dd>
452 <dd>Check every atom in the box when constructing a new neighbor list
454 </dl></dd>
461 <dd>Use no periodic boundary conditions, ignore the box.
465 and particle decomposition instead of domain decomposition.</dd>
467 <dd>Use periodic boundary conditions in x and y directions only.
470 Without walls or with only one wall the system size is infinite
471 in the z direction. Therefore pressure coupling or Ewald summation
472 methods can not be used.
473 These disadvantages do not apply when two walls are used.</dd>
474 </dl></dd>
481 <dd>for systems with molecules that couple to themselves through
482 the periodic boundary conditions, this requires a slower PBC algorithm
483 and molecules are not made whole in the output</dd>
484 </dl></dd>
490 (for performance reasons), particle pairs not in the pair list can occasionally
492 generates energy drift. In a constant-temperature ensemble, the drift can be
494 homogeneous particle distribution, hence the drift might be slightly
495 underestimated for multi-phase systems. For longer pair-list life-time
497 between particles are ignored. Combined with cancellation of errors,
498 the actual energy drift is usually one to two orders of magnitude smaller.
499 Note that the generated buffer size takes into account that
500 the GROMACS pair-list setup leads to a reduction in the drift by
501 a factor 10, compared to a simple particle-pair based list.
502 Without dynamics (energy minimization etc.), the buffer is 5% of the cut-off.
503 For dynamics without temperature coupling or to override the buffer size,
512 <dd>Cut-off distance for the long-range neighbor list.
513 This parameter is only relevant for a twin-range cut-off setup
514 with switched potentials. In that case a buffer region is required to account
515 for the size of charge groups. In all other cases this parameter
516 is automatically set to the longest cut-off distance.</dd>
517 </dl>
521 <hr>
523 <dl>
537 The relative accuracy of direct/reciprocal space
539 <br>
541 and is thus extremely slow for large systems. It is included mainly for
542 reference - in most cases PME will perform much better.</dd>
545 <dd>Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct space is similar
546 to the Ewald sum, while the reciprocal part is performed with
549 nm and cubic interpolation the electrostatic forces have an accuracy
551 might try 0.15 nm. When running in parallel the interpolation
552 parallelizes better than the FFT, so try decreasing grid dimensions
553 while increasing interpolation.</dd>
556 <dd>Particle-Particle Particle-Mesh algorithm with analytical derivative
557 for for long range electrostatic interactions. The method and code
558 is identical to SPME, except that the influence function is optimized
559 for the grid. This gives a slight increase in accuracy.</dd>
561 <dt><b>Reaction-Field electrostatics<!--QuietIdx-->reaction-field electrostatics<!--EQuietIdx--></b></dt>
571 The ionic strength is computed from the number of charged
573 The temperature for the GRF potential is set with
577 <dd>In GROMACS, normal reaction-field electrostatics with
580 by making the potential zero beyond the cut-off. It can only
582 because only for that value the force vanishes at the cut-off.
584 to accommodate for the size of charge groups and diffusion
585 between neighbor list updates. This, and the fact that table lookups
587 computationally more expensive than normal reaction-field.</dd>
591 GROMACS versions before 3.3. No reaction-field correction is applied
592 to excluded atom pairs and self pairs.
595 interaction is up to a few percent of the total electrostatic
596 energy and causes a minor difference in the forces and the pressure.</dd>
601 which has a similar potential shape, but has a physical interpretation
602 and has better energies due to the exclusion correction terms.
603 </dd>
606 <dd>The Coulomb
607 potential is decreased over the whole range, using the definition
608 from the Encad simulation package.</dd>
612 Switching the Coulomb potential can lead to serious artifacts,
618 repulsion, dispersion and Coulomb. When pair interactions are present,
620 the pair interactions. When the same interactions should be used
621 for non-bonded and pair interactions the user can specify the same
622 file name for both table files.
623 These files should contain 7
634 and should be uniformly spaced. For the pair interactions the table
635 length in the file will be used.
636 The optimal spacing, which is used for non-user tables,
640 in the printed manual.</dd>
643 <dd>A combination of PME and a switch function for the direct-space part
645 This is mainly useful constant energy simulations (note that using
647 </dd>
650 <dd>A combination of PME and user tables (see above).
653 Because of this subtraction the user tables should contain
657 <dd>A combination of PME-User and a switching function (see above).
658 The switching function is applied to final particle-particle interaction,
659 i.e. both to the user supplied function and the PME Mesh correction part.</dd>
661 </dl></dd>
675 <dd>The relative dielectric constant of the reaction field.
676 This is only used with reaction-field electrostatics.
678 </dl>
681 <hr>
683 <dl>
691 <dd>The LJ (not Buckingham) potential is decreased over the whole
695 charge groups and diffusion between neighbor list
696 updates.</dd>
699 <dd>The LJ (not Buckingham)
702 are continuously smooth, but be aware that all switch functions will give rise
703 to a bulge (increase) in the force (since we are switching the potential).
706 between neighbor list updates.</dd>
709 <dd>The LJ (not Buckingham)
710 potential is decreased over the whole range, using the definition
711 from the Encad simulation package.</dd>
717 cut-off in the user-defined function.
720 </dl></dd>
734 and Pressure</dd>
736 <dd>apply long range dispersion corrections for Energy
737 only</dd>
738 </dl>
739 </dl>
742 <hr>
744 <dl>
746 <dd>Extension of the non-bonded potential lookup tables beyond the largest cut-off distance.
747 The value should be large enough to account for charge group sizes
748 and the diffusion between neighbor-list updates.
749 Without user defined potential the same table length is used
751 which are always tabulated irrespective of the use of
752 tables for the non-bonded interactions. </dd>
755 <dd>When user tables are used for electrostatics and/or VdW,
756 here one can give pairs of energy groups for which seperate
757 user tables should be used.
758 The two energy groups will be appended to the table file name,
764 energy group pairs.
765 </dd>
766 </dl>
769 <hr>
771 <dl>
773 <dd>For ordinary Ewald, the ratio of the box dimensions and the spacing
774 determines a lower bound for the number of wave vectors to use in each
775 (signed) direction. For PME and P3M, that ratio determines a lower bound
776 for the number of Fourier-space grid points that will be used along that
777 axis. In all cases, the number for each direction can be overridden by
779 For optimizing the relative load of the particle-particle interactions
780 and the mesh part of PME, it is useful to know that
781 the accuracy of the electrostatics remains nearly constant
782 when the Coulomb cut-off and the PME grid spacing are scaled
783 by the same factor.</dd>
787 <dd>Grid size when using PME or P3M. These values override
796 <dd>The relative strength of the Ewald-shifted direct potential at
798 Decreasing this will give a more accurate direct sum,
799 but then you need more wave vectors for the reciprocal sum.</dd>
808 dimension to produce a pseudo-2D summation.
811 the slab height is usually ok)
812 and use this option.</dd>
813 </dl></dd>
817 default value of zero means it is turned off. Turn it on by setting it to the value
818 of the relative permittivity of the imaginary surface around your infinite system. Be
819 careful - you shouldn't use this if you have free mobile charges in your system.
828 <dd>Calculate the optimal FFT plan for the grid at startup. This saves a
829 few percent for long simulations, but takes a couple of minutes
830 at start.</dd>
831 </dl></dd>
833 </dl>
836 <hr>
839 <dl>
845 <dd>Temperature coupling with a Berendsen-thermostat to a bath with
847 Several groups can be coupled separately, these are specified in the
850 <dd>Temperature coupling using a Nose-Hoover extended
851 ensemble. The reference temperature and coupling groups are selected
853 of the temperature fluctuations at equilibrium, which is slightly
854 different from a relaxation time.
855 For NVT simulations the conserved energy quantity is written
856 to energy and log file.</dd>
858 <dd>Temperature coupling using velocity rescaling with a stochastic term
860 This thermostat is similar to Berendsen coupling, with the same scaling
862 canonical ensemble is generated. The random seed is set with
865 For NVT simulations the conserved energy quantity is written
866 to the energy and log file.</dd>
867 </dl>
869 <dd>The frequency for coupling the temperature.
873 </dd>
875 <dd>the number of chained Nose-Hoover thermostats for velocity Verlet integrators, the leap-frog <b>md</b> integrator only supports 1. Data for the NH chain variables is not printed to the .edr, but can be using the <tt>GMX_NOSEHOOVER_CHAINS</tt> environment variable</dd>
883 </dl>
886 <hr>
889 <dl>
895 <dd>Exponential relaxation pressure coupling with time constant
897 argued that this does not yield a correct thermodynamic ensemble,
898 but it is the most efficient way to scale a box at the beginning
899 of a run.</dd>
901 <dd>Extended-ensemble pressure coupling where the box vectors are
902 subject to an equation of motion. The equation of motion for the atoms
903 is coupled to this. No instantaneous scaling takes place. As for
905 is the period of pressure fluctuations at equilibrium. This is
906 probably a better method when you want to apply pressure scaling
907 during data collection, but beware that you can get very large
908 oscillations if you are starting from a different pressure. For
909 simulations where the exact fluctation of the NPT ensemble are
910 important, or if the pressure coupling time is very short it may not
911 be appropriate, as the previous time step pressure is used in some
912 steps of the GROMACS implementation for the current time step pressure.</dd>
913 </dl></dd>
918 [ps] is the period of pressure fluctuations at equilibrium. This is
919 probably a better method when you want to apply pressure scaling
920 during data collection, but beware that you can get very large
921 oscillations if you are starting from a different pressure. Currently only supports isotropic scaling.</dd>
922 </dl></dd>
924 <dl>
929 The compressibility and reference pressure are set with
931 value is needed.</dd>
935 This can be useful for membrane simulations.
938 <dd>Idem, but 6 values are needed for <tt>xx</tt>, <tt>yy</tt>, <tt>zz</tt>, <tt>xy/yx</tt>, <tt>xz/zx</tt> and <tt>yz/zy</tt>
939 components, respectively.
940 When the off-diagonal compressibilities are set to zero,
941 a rectangular box will stay rectangular.
942 Beware that anisotropic scaling can lead to extreme deformation
943 of the simulation box.</dd>
945 <dd>Surface tension coupling for surfaces parallel to the xy-plane.
949 the number of surfaces [bar nm],
954 influences the convergence of the surface-tension, it can also be set to zero
955 to have a box with constant height.</dd>
956 </dl></dd>
959 <dd>The frequency for coupling the pressure.
963 </dd>
975 <dd>The reference coordinates for position restraints are not modified.
976 Note that with this option the virial and pressure will depend on the absolute
977 positions of the reference coordinates.</dd>
981 <dd>Scale the center of mass of the reference coordinates with the scaling matrix of the pressure coupling. The vectors of each reference coordinate to the center of mass are not scaled. Only one COM is used, even when there are multiple molecules with position restraints. For calculating the COM of the reference coordinates in the starting configuration, periodic boundary conditions are not taken into account.
982 </dl></dd>
983 </dd>
984 </dl>
987 <hr>
990 Simulated annealing is controlled separately for each temperature group in GROMACS. The reference temperature is a piecewise linear function, but you can use an arbitrary number of points for each group, and choose either a single sequence or a periodic behaviour for each group. The actual annealing is performed by dynamically changing the reference temperature used in the thermostat algorithm selected, so remember that the system will usually not instantaneously reach the reference temperature!
991 <dl>
998 <dd>A single sequence of annealing points. If your simulation is longer than the time of the last point, the temperature will be coupled to this constant value after the annealing sequence has reached the last time point.</dd>
1000 <dd>The annealing will start over at the first reference point once the last reference time is reached. This is repeated until the simulation ends.
1001 </dd>
1002 </dl>
1005 <dd>A list with the number of annealing reference/control points used for
1006 each temperature group. Use 0 for groups that are not annealed. The number of entries should equal the number of temperature groups.</dd>
1009 <dd>List of times at the annealing reference/control points for each group. If you are using periodic annealing, the times will be used modulo the last value, i.e. if the values are 0, 5, 10, and 15, the coupling will restart at the 0ps value after 15ps, 30ps, 45ps, etc. The number of entries should equal the sum of the numbers given in <tt>annealing-npoints</tt>.</dd>
1012 <dd>List of temperatures at the annealing reference/control points for each group. The number of entries should equal the sum of the numbers given in <tt>annealing-npoints</tt>.</dd>
1013 <br>
1014 Confused? OK, let's use an example. Assume you have two temperature groups, set the group selections to <tt>annealing = single periodic</tt>, the number of points of each group to <tt>annealing-npoints = 3 4</tt>, the times to <tt>annealing-time = 0 3 6 0 2 4 6</tt> and finally temperatures to <tt>annealing-temp = 298 280 270 298 320 320 298</tt>.
1015 The first group will be coupled to 298K at 0ps, but the reference temperature will drop linearly to reach 280K at 3ps, and then linearly between 280K and 270K from 3ps to 6ps. After this is stays constant, at 270K. The second group is coupled to 298K at 0ps, it increases linearly to 320K at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it decreases to 298K, and then it starts over with the same pattern again, i.e. rising linearly from 298K to 320K between 6ps and 8ps. Check the summary printed by <tt>grompp</tt> if you are unsure!
1016 </dl>
1019 <hr>
1022 <dl>
1026 <dd> Do not generate velocities. The velocities are set to zero
1027 when there are no velocities in the input structure file.</dd>
1032 </dl></dd>
1036 <dd>used to initialize random generator for random velocities,
1038 the process ID number.
1039 </dl>
1042 <hr>
1045 <dl>
1049 <dd>No constraints except for those defined explicitly in the topology,
1050 i.e. bonds are represented by a harmonic (or other) potential
1052 and angles by a harmonic (or other) potential.
1058 <dd>Convert all bonds and additionally the angles that involve H-atoms
1059 to bond-constraints.</dd>
1062 </dl>
1067 <dd>LINear Constraint Solver.
1068 With domain decomposition the parallel version P-LINCS is used.
1069 The accuracy in set with
1071 for the matrix inversion.
1072 After the matrix inversion correction the algorithm does
1073 an iterative correction to compensate for lengthening due to rotation.
1074 The number of such iterations can be controlled with
1079 LINCS should not be used with coupled angle constraints.
1080 </dd>
1082 <dd>SHAKE is slightly slower and less stable than LINCS, but does work with
1083 angle constraints.
1085 for ``normal'' MD. SHAKE does not support constraints between atoms
1086 on different nodes, thus it can not be used with domain decompositon
1087 when inter charge-group constraints are present.
1088 SHAKE can not be used with energy minimization.
1089 </dd>
1090 </dl></dd>
1097 <dd>do not apply constraints to the start configuration
1098 and do not reset shells, useful for exact coninuation and reruns</dd>
1099 </dl></dd>
1105 <dd>Highest order in the expansion of the constraint coupling matrix.
1106 When constraints form triangles, an additional expansion of the same
1107 order is applied on top of the normal expansion only for the couplings
1108 within such triangles.
1110 needed for large time-steps with virtual sites or BD.
1111 For accurate energy minimization an order of 8 or more might be required.
1112 With domain decomposition, the cell size is limited by the distance
1118 <dd>Number of iterations to correct for rotational lengthening in LINCS.
1119 For normal runs a single step is sufficient, but for NVE
1120 runs where you want to conserve energy accurately or for accurate
1121 energy minimization you might want to increase it to 2.
1131 </dl></dd>
1132 </dl>
1135 <hr>
1137 <dl>
1139 <dd>Pairs of energy groups for which all non-bonded interactions are
1142 <br>
1144 <br>
1145 would give only the non-bonded interactions between the protein and the
1146 solvent. This is especially useful for speeding up energy calculations with
1148 </dl>
1151 <hr>
1153 <dl>
1158 (it is usually best to use semiisotropic pressure coupling with
1162 added automatically to monitor the interaction of energy groups
1163 with each wall.
1167 <dd>the atom type name in the force field for each wall.
1168 By (for example) defining a special wall atom type in the topology with its
1169 own combination rules, this allows for independent tuning of the interaction
1170 of each atomtype with the walls.</dd>
1179 <dt><b>table</b></dt><dd>user defined potentials indexed with the z distance from the wall, the tables are read analogously to
1181 where the first name is for a ``normal'' energy group and the second name
1183 only the dispersion and repulsion columns are used</dd>
1184 </dl></dd>
1186 <dd>Below this distance from the wall the potential is continued
1187 linearly and thus the force is constant. Setting this option to
1188 a postive value is especially useful for equilibration when some atoms
1189 are beyond a wall.
1191 a fatal error is generated when atoms are beyond a wall.
1192 </dd>
1194 <dd>the number density of the atoms for each wall for wall types
1197 <dd>The scaling factor for the third box vector for Ewald summation only,
1198 the minimum is 2.
1201 The empty layer in the box serves to decrease the unphysical Coulomb
1202 interaction between periodic images.
1203 </dl>
1206 <hr>
1208 <dl>
1212 <dd>No center of mass pulling.
1213 All the following pull options will be ignored
1216 <dd>Center of mass pulling using an umbrella potential
1217 between the reference group and one or more groups.</dd>
1219 <dd>Center of mass pulling using a constraint
1220 between the reference group and one or more groups.
1222 that a rigid constraint is applied instead of a harmonic potential.</dd>
1224 <dd>Center of mass pulling using a linear potential and therefore
1225 a constant force. For this option there is no reference position
1227 are not used.</dd>
1228 </dl></dd>
1232 <dd>Pull along the vector connecting the two groups.
1238 half the box size. With this geometry the box should not be dynamic
1239 (e.g. no pressure scaling) in the pull dimensions and the pull force
1240 is not added to virial.</dd>
1242 <dd>Designed for pulling with respect to a layer where the reference COM
1243 is given by a local cylindrical part of the reference group.
1245 From the reference group a cylinder is selected around the axis going
1250 Note that the radii should be smaller than half the box size.
1251 For tilted cylinders they should be even smaller than half the box size
1252 since the distance of an atom in the reference group
1253 from the COM of the pull group has both a radial and an axial component.
1255 <dd>Pull to the position of the reference group plus
1257 </dl></dd>
1261 to the output files</dd>
1274 </dl>
1280 <dd>The number of pull groups, not including the reference group.
1281 If there is only one group, there is no difference in treatment
1282 of the reference and pulled group (except with the cylinder geometry).
1283 Below only the pull options for the reference group (ending on 0)
1284 and the first group (ending on 1) are given,
1285 further groups work analogously, but with the number 1 replaced
1286 by the group number.</dd>
1288 <dd>The name of the reference group. When this is empty an absolute reference
1290 translation invariant and one should think about what to do with
1299 <dd>Optional relative weights which are multiplied with the masses of the atoms
1301 or the number of atoms in the pull group.</dd>
1303 <dd>The reference atom for the treatment of periodic boundary conditions
1304 inside the group
1305 (this has no effect on the treatment of the pbc between groups).
1306 This option is only important when the diameter of the pull group
1307 is larger than half the shortest box vector.
1308 For determining the COM, all atoms in the group are put at their periodic image
1310 A value of 0 means that the middle atom (number wise) is used.
1312 A value of -1 turns on cosine weighting, which is useful for a group
1313 of molecules in a periodic system, e.g. a water slab (see Engin et al.
1322 <dt><b>pull-k1: (0) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
1323 <dd>The force constant. For umbrella pulling this is the harmonic force
1325 this is the force constant of the linear potential, and thus minus (!)
1327 <dt><b>pull-kB1: (pull-k1) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
1331 </dl>
1334 <hr>
1336 <dl>
1342 <dd>simple (per-molecule) distance restraints.
1344 <dd>distance restraints over an ensemble of molecules in one
1345 simulation box. Normally, one would perform ensemble averaging over
1348 coordinates and/or velocities.
1351 </dd>
1352 </dl></dd>
1358 <dd>the forces are the derivative of the restraint potential,
1361 </dl></dd>
1365 <dd>the violation used in the calculation of the restraint force is the
1366 time-averaged violation </dd>
1368 <dd>the violation used in the calculation of the restraint force is the
1369 square root of the product of the time-averaged violation and the instantaneous violation</dd>
1370 </dl></dd>
1373 <dd>force constant for distance restraints, which is multiplied by a
1375 column of the interaction in the topology file.</dd>
1378 <dd>time constant for distance restraints running average. A value of zero turns off time averaging.</dd>
1381 <dd>period between steps when the running time-averaged and instantaneous distances
1382 of all atom pairs involved in restraints are written to the energy file
1383 (can make the energy file very large)</dd>
1391 <dd>use orientation restraints, ensemble averaging can be performed
1393 </dl>
1395 <dd>force constant for orientation restraints, which is multiplied by a
1396 (possibly) different weight factor for each restraint, can be set to zero to
1397 obtain the orientations from a free simulation</dd>
1399 <dd>time constant for orientation restraints running average. A value of zero turns off time averaging.</dd>
1401 <dd>fit group for orientation restraining. This group of atoms is used
1403 reference orientation. The reference orientation is the starting
1404 conformation of the first subsystem. For a protein, backbone is a reasonable
1405 choice</dd>
1407 <dd>period between steps when the running time-averaged and instantaneous orientations
1408 for all restraints, and the molecular order tensor are written to the energy file
1409 (can make the energy file very large)</dd>
1410 </dl>
1413 <hr>
1416 <dl>
1423 and write the derivative of the Hamiltonian with respect to lambda (as specified with <b>dhdl-derivatives</b>), or the Hamiltonian differences with respect to other lambda values (as specified with <b>foreign-lambda</b>) to
1424 the energy file and/or to <tt>dhdl.xvg</tt>, where they can be processed by, for example <tt>g_bar</tt>.
1425 The potentials, bond-lengths and angles are interpolated linearly as
1427 potentials are used for the LJ and Coulomb interactions.</dd>
1428 </dl></dd>
1430 <dd>starting value for lambda (float). Generally, this should only be used with slow growth. In other cases, <b>init-lambda-state</b> should be specified instead.</dd>
1432 <dd>starting value for the lambda state (integer). Specified which columm of the lambda vector should be used.</dd>
1436 <dd>Zero, one or more lambda values for which Delta H values will
1438 Only the electrostatic interactions are controlled with this component of the lambda vector.</dd>
1440 <dd>Zero, one or more lambda values for which Delta H values will
1442 Only the van der Waals interactions are controlled with this component of the lambda vector.</dd>
1444 <dd>Zero, one or more lambda values for which Delta H values will
1446 Only the bonded interactions are controlled with this component of the lambda vector.</dd>
1448 <dd>Zero, one or more lambda values for which Delta H values will
1450 Only the restraint interactions are controlled with this component of the lambda vector.</dd>
1452 <dd>Zero, one or more lambda values for which Delta H values will
1454 Only the particle masses are controlled with this component of the lambda vector.</dd>
1456 <dd>Zero, one or more lambda values for which Delta H values will
1458 Only the temperatures controlled with this component of the lambda vector.
1459 Note that these lambdas should not be used for replica exchange, only for simulated tempering.</dd>
1461 <dd>Zero, one or more lambda values for which Delta H values will
1463 Free energy differences between different lambda values can then
1464 be determined with <tt>g_bar</tt>. <b>fep-lambdas</b> is different from the other -lambdas keywords because
1467 <dd>If yes (the default), the derivatives of the Hamiltonian with respect to lambda at each <b>nstdhdl</b> step are written out. These values are needed for interpolation of linear energy differences with <tt>g_bar</tt> (although the same can also be achieved with the right <b>foreign lambda</b> setting, that may not be as flexible), or with thermodynamic integration</dd>
1470 the LJ and Coulomb interactions</dd>
1472 <dd>the power of the radial term in the soft-core equation. Possible values are 6 and 48. 6 is more standard, and is the default. When 48 is used, then sc-alpha should generally be much lower (between 0.001 and 0.003).</dd>
1474 <dd>Whether to apply the soft core free energy interations to the Columbic interaction. Default is no, as it is generally
1475 more efficient to turn of the Coulomic interactions linearly before turning off electrostatic interactions.</dd>
1477 <dd>the power for lambda in the soft-core function,
1480 <dd>the soft-core sigma for particles which have a C6 or C12 parameter equal
1483 <dd>Here one can supply a molecule type (as defined in the topology)
1484 for calculating solvation or coupling free energies.
1486 in the system. This can be useful for equilibrating a system
1487 starting from (nearly) random coordinates.
1489 The Van der Waals interactions and/or charges in this molecule type can be
1492 one of several copies of a molecule, you need to copy and rename
1493 the molecule definition in the topology.</dd>
1501 <dd>the Van der Waals interactions are turned at lambda=0; soft-core interactions will be required to avoid singularities
1503 <dd>the Van der Waals interactions are turned off and the charges are zero at lambda=0; soft-core interactions will be required to avoid singularities
1504 </dl>
1510 <dd>All intra-molecular non-bonded interactions for moleculetype <b>couple-moltype</b> are replaced by exclusions and explicit pair interactions. In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects.
1512 <dd>The intra-molecular Van der Waals and Coulomb interactions are also turned on/off. This can be useful for partitioning free-energies of relatively large molecules, where the intra-molecular non-bonded interactions might lead to kinetically trapped vacuum conformations. The 1-4 pair interactions are not turned off.
1513 </dl>
1515 <dd>the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg,
1518 <dd>the frequency at which energies at other values of lambda are calculated. If not specified, set to be the same as <b>nstdhdl</b>. Should be a multiple of <b>nstcalcenergy</b>. If replica exchange is chosen, then -replex must also be a multiple of <b>nstfep</b></dd>
1522 <dd>the free energy values that are calculated (as specified with the <b>foreign-lambda</b> and <b>dhdl-derivatives</b> settings) are written out to a separate file, with the default name <tt>dhdl.xvg</tt>. This file can be used directly with <tt>g_bar</tt>.</dd>
1524 <dd>The free energy values are written out to the energy output file (<tt>ener.edr</tt>, in accumulated blocks at every <b>nstenergy</b> steps), where they can be extracted with <tt>g_energy</tt> or used directly with <tt>g_bar</tt>.</dd>
1525 </dl>
1527 <dd>If nonzero, specifies the size of the histogram into which the Delta H values (specified with <b>foreign-lambda</b>) and the derivative dH/dl values are binned, and written to ener.edr. This can be used to save disk space while calculating free energy differences. One histogram gets written for each <b>foreign lambda</b> and two for the dH/dl, at every <b>nstenergy</b> step. Be aware that incorrect histogram settings (too small size or too wide bins) can introduce errors. Do not use histograms unless you're certain you need it.</dd>
1529 <dd>Specifies the bin width of the histograms, in energy units. Used in conjunction with <b>dh-hist-size</b>. This size limits the accuracy with which free energies can be calculated. Do not use histograms unless you're certain you need it.</dd>
1530 </dl>
1532 <hr>
1535 <dl>
1543 <dd> Uses the Metropolis weights to update the expanded ensemble weight of the state.
1546 <dd> Uses the Barker transition critera to update the expanded ensemble weight of the state.</dd>
1548 <dd>Uses the Wang-Landau algorithm (in state space) to update the expanded ensemble weights.</dd>
1550 <dd>Uses the minimum variance updating method of Escobedo et al to update the expanded ensemble weights. Weights
1551 will not be the free energies, but will rather emphasize states that need more sampling to give even uncertainty.
1552 </dl>
1558 <dd> Randomly chooses a new state up or down, then uses the Metropolis critera to decide whether to accept or reject:
1561 <dd> Randomly chooses a new state up or down, then uses the Barker transition critera to decide whether to accept or reject: exp(-beta_new u_new)/[exp(-beta_new u_new)+exp(-beta_old u_old)] </dd>
1563 <dd> Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to
1564 decide which state to move to.</dd>
1566 <dd>
1567 <dd> Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to
1568 decide which state to move to, EXCLUDING the current state, then uses a rejection step to ensure detailed
1569 balance. Always more efficient that Gibbs, though marginally so in many situations.</dd>
1570 </dl>
1573 <dd> random seed to use for Monte Carlo moves in state space. If not specified, <b>ld-seed</b> is used instead. </dd>
1575 <dd> Temperature used for acceptance/rejection for Monte Carlo moves. If not specified, the temperature of the
1586 <dd>Frequency of outputting the expanded ensemble transition matrix. A negative number means it will only be printed at the end of the simulation.<dd>
1598 </dl>
1601 <hr>
1604 <dl>
1607 all atoms in groups Protein and Sol will experience constant acceleration
1613 opposite).</dd>
1615 <dd>Groups that are to be frozen (i.e. their X, Y, and/or Z position will
1617 which dimension the freezing applies.
1618 To avoid spurious contibrutions to the virial and pressure due to large
1619 forces between completely frozen atoms you need to use
1621 Note that coordinates of frozen atoms are not scaled by pressure-coupling
1622 algorithms.</dd>
1627 can move only in Z direction. The particles in the second group can
1628 move in any direction).</dd>
1630 <dd>the amplitude of the acceleration profile for calculating the
1632 The acceleration is in the X-direction and the magnitude is
1634 Two terms are added to the energy file:
1637 <dd>The velocities of deformation for the box elements:
1638 a(x) b(y) c(z) b(x) c(x) c(y). Each step the box elements
1640 box(ts)+(t-ts)*deform, off-diagonal elements are corrected
1641 for periodicity. The coordinates are transformed accordingly.
1642 Frozen degrees of freedom are (purposely) also transformed.
1643 The time ts is set to t at the first step and at steps at which
1644 x and v are written to trajectory to ensure exact restarts.
1645 Deformation can be used together with semiisotropic or anisotropic
1646 pressure coupling when the appropriate compressibilities are set to zero.
1649 or a liquid.</dd>
1650 </dl>
1653 <hr>
1656 <dl>
1661 the second number: the strength of the electric field in
1663 the third number: the phase of the cosine, you can enter any number here
1664 since a cosine of frequency zero has no phase.</dd>
1667 </dl>
1668 <br>
1670 <hr>
1674 <dl>
1680 <dd>Do a QM/MM simulation. Several groups can be described at
1681 different QM levels separately. These are specified in
1683 initio</i> theory at which the groups are described is specified
1685 groups at different levels of theory is only possible with the ONIOM
1687 </dl></dd>
1697 theory. The rest of the system is described at the MM level. The QM
1698 and MM subsystems interact as follows: MM point charges are included
1699 in the QM one-electron hamiltonian and all Lennard-Jones interactions
1700 are described at the MM level.</dd>
1702 <dd>The interaction between the subsystem is described using the ONIOM
1703 method by Morokuma and co-workers. There can be more than one <b>QMMM-grps</b> each modeled at a different level of QM theory
1705 </dd></dl></dd>
1708 <dd>Method used to compute the energy and gradients on the QM
1709 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
1710 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
1715 <dd>Basis set used to expand the electronic wavefuntion. Only Gaussian
1722 ONIOM layer needs to be specified separately.</dd>
1727 to be specified separately.</dd>
1730 <dd>The number of orbitals to be included in the active space when
1731 doing a CASSCF computation.</dd>
1734 <dd>The number of electrons to be included in the active space when
1735 doing a CASSCF computation.</dd>
1740 <dd>No surface hopping. The system is always in the electronic
1741 ground-state.</dd>
1743 <dd>Do a QM/MM MD simulation on the excited state-potential energy
1745 system hits the conical intersection hyperline in the course the
1746 simulation. This option only works in combination with the CASSCF
1747 method.</dd>
1748 </dl>
1749 </dl>
1752 <hr>
1755 <dl>
1761 <dd>Do a simulation with implicit solvent using the Generalized Born formalism.
1762 Three different methods for calculating the Born radii are available, Still, HCT and
1765 </dl>
1775 </dl>
1778 <dd>Frequency to (re)-calculate the Born radii. For most practial purposes,
1779 setting a value larger than 1 violates energy conservation and leads to
1780 unstable trajectories.</dd>
1792 <dd>Scale factors for the OBC model. Default values are OBC(II).
1796 <dd>Distance for the di-electric offset when calculating the Born radii. This is
1797 the offset between the center of each atom the center of the polarization energy
1798 for the corresponding atom</dd>
1805 <dd>No non-polar solvation calculation done. For GBSA only the polar part gets
1806 calculated</dd>
1807 </dl>
1811 Note that if this default value is not changed
1813 of radii algorithm (0.0049 kcal/mol/Angstrom<sup>2</sup> for Still, 0.0054 kcal/mol/Angstrom<sup>2</sup>
1814 for HCT/OBC)
1816 Setting it to 0 will while using an sa-algorithm other than None means
1817 no non-polar calculations are done.
1818 </dd>
1819 </dl>
1822 <hr>
1825 <dl>
1831 <dd>Do an AdResS simulation with weight equal 1, which is equivalent to an explicit (normal) MD simulation. The difference to disabled AdResS is that the AdResS variables are still read-in and hence are defined.</dd>
1833 <dd>Do an AdResS simulation with a constant weight, <b>adress-const-wf</b> defines the value of the weight</dd>
1835 <dd>Do an AdResS simulation with simulation box split in x-direction, so basically the weight is only a function of the x coordinate and all distances are measured using the x coordinate only.</dd>
1838 </dl></dd>
1846 <dd>Position of the center of the explicit zone. Periodic boundary conditions apply for measuring the distance from it.</dd>
1848 <dd>The names of the coarse-grained energy groups. All other energy groups are considered explicit and their interactions will be automatically excluded with the coarse-grained groups.</dd>
1859 </dl></dd>
1865 <dd>Apply thermodynamic force interface correction. The table can be specified using the <tt>-tabletf</tt> option of <tt>mdrun</tt>. The table should contain the potential and force (acting on molecules) as function of the distance from <b>adress-reference-coords</b>.</dd>
1866 </dl></dd>
1868 <dd>The names of the energy groups to which the <b>thermoforce</b> is applied if enabled in <b>adress-interface-correction</b>. If no group is given the default table is applied.</dd>
1870 <dd>Cap the force in the hybrid region, useful for big molecules. 0 disables force capping.</dd>
1871 </dl>
1874 <hr>
1877 <dl>
1881 <dd>These you can use if you modify code. You can pass integers and
1882 reals to your subroutine. Check the inputrec definition in
1885 </dl>
1888 <hr>
1891 <P>
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