1 <TITLE>mdp options</TITLE>
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12 <H3>Table of Contents</H3>
15 <li><A HREF="#general"><b>General remarks</b></A>
17 <li><A HREF="#pp"><b>preprocessing</b></A> (include, define)
18 <li><A HREF="#run"><b>run control</b></A> (integrator, tinit, dt, nsteps, init-step, comm-mode, nstcomm, comm-grps)
19 <li><A HREF="#ld"><b>langevin dynamics</b></A> (bd-fric, ld-seed)
20 <li><A HREF="#em"><b>energy minimization</b></A> (emtol, emstep, nstcgsteep)
21 <li><a HREF="#shellmd"><b>shell molecular dynamics</b></a>(emtol,niter,fcstep)
22 <li><a HREF="#tpi"><b>test particle insertion</b></a>(rtpi)
23 <li><A HREF="#out"><b>output control</b></A> (nstxout, nstvout, nstfout, nstlog, nstcalcenergy, nstenergy, nstxout-compressed, compressed-x-precision, compressed-x-grps, energygrps)
24 <li><A HREF="#nl"><b>neighbor searching</b></A> (cutoff-scheme, nstlist, nstcalclr, ns-type, pbc, periodic-molecules, verlet-buffer-tolerance, rlist, rlistlong)
25 <li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, coulomb-modifier, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
26 <li><A HREF="#vdw"><b>VdW</b></A> (vdwtype, vdw-modifier, rvdw-switch, rvdw, DispCorr)
27 <li><A HREF="#table"><b>tables</b></A> (table-extension, energygrp-table)
28 <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)
29 <li><A HREF="#tc"><b>Temperature coupling</b></A> (tcoupl, nsttcouple, tc-grps, tau-t, ref-t)
30 <li><A HREF="#pc"><b>Pressure coupling</b></A> (pcoupl, pcoupltype,
31 nstpcouple, tau-p, compressibility, ref-p, refcoord-scaling)
32 <li><A HREF="#sa"><b>simulated annealing</b></A> (annealing, annealing-npoints, annealing-time, annealing-temp)
33 <li><A HREF="#vel"><b>velocity generation</b></A> (gen-vel, gen-temp, gen-seed)
34 <li><A HREF="#bond"><b>bonds</b></A> (constraints, constraint-algorithm, continuation, shake-tol, lincs-order, lincs-iter, lincs-warnangle, morse)
35 <li><A HREF="#egexcl"><b>Energy group exclusions</b></A> (energygrp-excl)
36 <li><A HREF="#walls"><b>Walls</b></A> (nwall, wall-type, wall-r-linpot, wall-atomtype,
37 wall-density, wall-ewald-zfac)
38 <li><A HREF="#pull"><b>COM pulling</b></A> (pull, ...)
39 <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)
40 <li><A HREF="#free"><b>Free energy calculations</b></A> (free-energy, nstdhdl, dhdl-print-energy, init-lambda, delta-lambda, fep-lambdas, coul-lambdas, vdw-lambdas, bonded-lambdas, restraint-lambdas, mass-lambdas, temperature-lambdas, sc-alpha, sc-coul, sc-power, sc-r-power, sc-sigma, couple-moltype, couple-lambda0, couple-lambda1, couple-intramol)
41 <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, 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)
42 <li><A HREF="#neq"><b>Non-equilibrium MD</b></A> (acc-grps, accelerate, freezegrps, freezedim, cos-acceleration, deform)
43 <li><A HREF="#ef"><b>Electric fields</b></A> (E-x, E-xt, E-y, E-yt, E-z, E-zt )
44 <li><A HREF="#qmmm"><b>Mixed quantum/classical dynamics</b></A> (QMMM, QMMM-grps, QMMMscheme, QMmethod, QMbasis, QMcharge, Qmmult, CASorbitals, CASelectrons, SH)
45 <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)
46 <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)
47 <li><A HREF="#user"><b>User defined thingies</b></A> (user1-grps, user2-grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
48 <li><A HREF="#idx"><b>Index</b></A>
54 <A NAME="general"><br>
58 Default values are given in parentheses. The first option in
59 the list is always the default option. Units are given in
60 square brackets The difference between a dash and an underscore
64 A <a href="mdp.html">sample <TT>.mdp</TT> file</a> is
65 available. This should be appropriate to start a normal
66 simulation. Edit it to suit your specific needs and desires. </P>
70 <h3>Preprocessing</h3>
73 <dt><b>include:</b></dt>
74 <dd>directories to include in your topology. Format:
75 <PRE>-I/home/john/mylib -I../otherlib</PRE></dd>
76 <dt><b>define:</b></dt>
77 <dd>defines to pass to the preprocessor, default is no defines. You can use
78 any defines to control options in your customized topology files. Options
79 that are already available by default are:
82 <dd>Will tell <tt>grompp</tt> to include flexible water in stead of rigid water into your
83 topology, this can be useful for normal mode analysis.</dd>
85 <dd>Will tell <tt>grompp</tt> to include posre.itp into your topology, used for
86 <!--Idx-->position restraint<!--EIdx-->s.</dd>
95 <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>
98 <dd>A leap-frog algorithm<!--QuietIdx-->leap-frog integrator<!--EQuietIdx-->
99 for integrating Newton's equations of motion.</dd>
100 <dt><b>md-vv</b></dt>
101 <dd>A velocity Verlet algorithm for integrating Newton's equations of motion.
102 For constant NVE simulations started from corresponding points in the same trajectory, the trajectories
103 are analytically, but not binary, identical to the <b>md</b> leap-frog integrator. The the kinetic
104 energy, which is determined from the whole step velocities and is therefore
105 slightly too high. The advantage of this integrator is more accurate,
106 reversible Nose-Hoover and Parrinello-Rahman coupling integration
107 based on Trotter expansion, as well as (slightly too small) full step velocity
108 output. This all comes at the cost off extra computation, especially with
109 constraints and extra communication in parallel. Note that for nearly all
110 production simulations the <b>md</b> integrator is accurate enough.
112 <dt><b>md-vv-avek</b></dt>
113 <dd>A velocity Verlet algorithm identical to <b>md-vv</b>, except that
114 the kinetic energy is determined as the average of
115 the two half step kinetic energies as in the <b>md</b> integrator, and this thus more accurate.
116 With Nose-Hoover and/or Parrinello-Rahman coupling this comes with
117 a slight increase in computational cost.
120 <dd> An accurate leap-frog stochastic dynamics integrator.
121 Four Gaussian random number are required
122 per integration step per degree of freedom. With constraints,
123 coordinates needs to be constrained twice per integration step.
124 Depending on the computational cost of the force calculation,
125 this can take a significant part of the simulation time.
126 The temperature for one or more groups of atoms
127 (<b><A HREF="#tc">tc-grps</A></b>)
128 is set with <b><A HREF="#tc">ref-t</A></b> [K],
129 the inverse friction constant for each group is set with
130 <b><A HREF="#tc">tau-t</A></b> [ps].
131 The parameter <b><A HREF="#tc">tcoupl</A></b> is ignored.
132 The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.
133 When used as a thermostat, an appropriate value for <b>tau-t</b> is 2 ps,
134 since this results in a friction that is lower than the internal friction
135 of water, while it is high enough to remove excess heat
136 (unless <b>cut-off</b> or <b>reaction-field</b> electrostatics is used).
137 NOTE: temperature deviations decay twice as fast as with
138 a Berendsen thermostat with the same <b>tau-t</b>.</dd>
140 <dd> An efficient leap-frog stochastic dynamics integrator.
141 This integrator is equivalent to <b>sd</b>, except that it requires
142 only one Gaussian random number and one constraint step and is therefore
143 significantly faster. Without constraints the accuracy is the same as <b>sd</b>.
144 With constraints the accuracy is significantly reduced, so then <b>sd</b>
145 will often be preferred.</dd>
147 <dd>An Euler integrator for Brownian or position Langevin dynamics, the
148 velocity is the force divided by a friction coefficient
149 (<b><A HREF="#ld">bd-fric</A></b> [amu ps<sup>-1</sup>])
150 plus random thermal noise (<b><A HREF="#tc">ref-t</A></b>).
151 When <b><A HREF="#ld">bd-fric</A></b><tt>=0</tt>, the friction coefficient for each
152 particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>, as for the
153 integrator <tt>sd</tt>.
154 The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.</dd>
156 <dt><b>steep</b></dt>
157 <dd>A <!--Idx-->steepest descent<!--EIdx--> algorithm for energy
158 minimization. The maximum step size is <b><A HREF="#em">emstep</A></b>
159 [nm], the tolerance is <b><A HREF="#em">emtol</A></b> [kJ
160 mol<sup>-1</sup> nm<sup>-1</sup>].</dd>
162 <dd>A <!--Idx-->conjugate gradient<!--EIdx--> algorithm for energy
163 minimization, the tolerance is <b>emtol</b> [kJ mol<sup>-1</sup>
164 nm<sup>-1</sup>]. CG is more efficient when a steepest descent step
165 is done every once in a while, this is determined by
166 <b><A HREF="#em">nstcgsteep</A></b>.
167 For a minimization prior to a normal mode analysis, which requires
168 a very high accuracy, GROMACS should be compiled in double precision.</dd>
169 <dt><b>l-bfgs</b></dt>
170 <dd>A <!--Idx-->quasi-Newtonian<!--EIdx--> algorithm for energy minimization
171 according to the low-memory Broyden-Fletcher-Goldfarb-Shanno approach.
172 In practice this seems to converge faster than Conjugate Gradients, but due
173 to the correction steps necessary it is not (yet) parallelized.
176 <dd>Normal mode analysis<!--QuietIdx-->normal-mode analysis<!--EQuietIdx--> is performed
177 on the structure in the <tt>tpr</tt> file. GROMACS should be
178 compiled in double precision.</dd>
180 <dd> Test particle insertion. The last molecule in the topology
181 is the test particle. A trajectory should be provided with
182 the <tt>-rerun</tt> option of <tt>mdrun</tt>. This trajectory
183 should not contain the molecule to be inserted. Insertions
184 are performed <b>nsteps</b> times in each frame at random locations
185 and with random orientiations of the molecule. When <b>nstlist</b>
186 is larger than one, <b>nstlist</b> insertions are performed
187 in a sphere with radius <b><A HREF="#tpi">rtpi</A></b>
188 around a the same random location using the same neighborlist
189 (and the same long-range energy when <b>rvdw</b> or <b>rcoulomb</b>><b>rlist</b>,
190 which is only allowed for single-atom molecules).
191 Since neighborlist construction is expensive, one can perform several
192 extra insertions with the same list almost for free.
193 The random seed is set with <b><A HREF="#ld">ld-seed</A></b>.
194 The temperature for the Boltzmann weighting is set with
195 <b><A HREF="#tc">ref-t</A></b>, this should match the temperature
196 of the simulation of the original trajectory.
197 Dispersion correction is implemented correctly for tpi.
198 All relevant quantities are written to the file specified with
199 the <tt>-tpi</tt> option of <tt>mdrun</tt>.
200 The distribution of insertion energies is written to the file specified with
201 the <tt>-tpid</tt> option of <tt>mdrun</tt>.
202 No trajectory or energy file is written.
203 Parallel tpi gives identical results to single node tpi.
204 For charged molecules, using PME with a fine grid is most accurate
205 and also efficient, since the potential in the system only needs
206 to be calculated once per frame.
209 <dd> Test particle insertion into a predefined cavity location.
210 The procedure is the same as for <b>tpi</b>, except that one coordinate
211 extra is read from the trajectory, which is used as the insertion location.
212 The molecule to be inserted should be centered at 0,0,0. Gromacs does
213 not do this for you, since for different situations a different
214 way of centering might be optimal.
215 Also <b><A HREF="#tpi">rtpi</A></b> sets the radius for the sphere
216 around this location. Neighbor searching is done only once per frame,
217 <b>nstlist</b> is not used.
218 Parallel tpic gives identical results to single node tpic.
221 <dt><b>tinit: (0) [ps]</b></dt>
222 <dd>starting time for your run (only makes sense for integrators <tt>md</tt>,
223 <tt>sd</tt> and <tt>bd</tt>)</dd>
224 <dt><b>dt: (0.001) [ps]</b></dt></dd>
225 <dd>time step for integration (only makes sense for integrators <tt>md</tt>,
226 <tt>sd</tt> and <tt>bd</tt>)</dd>
227 <dt><b>nsteps: (0)</b></dt>
228 <dd>maximum number of steps to integrate or minimize, -1 is no maximum</dd>
229 <dt><b>init-step: (0)</b></dt>
230 <dd>The starting step.
231 The time at an step i in a run is calculated as: t = <tt>tinit</tt> + <tt>dt</tt>*(<tt>init-step</tt> + i).
232 The free-energy lambda is calculated as: lambda = <tt>init-lambda</tt> + <tt>delta-lambda</tt>*(<tt>init-step</tt> + i).
233 Also non-equilibrium MD parameters can depend on the step number.
234 Thus for exact restarts or redoing part of a run it might be necessary to
235 set <tt>init-step</tt> to the step number of the restart frame.
236 <tt>gmx convert-tpr</tt> does this automatically.
238 <dt><b>comm-mode:</b></dt>
240 <dt><b>Linear</b></dt>
241 <dd>Remove center of mass translation</dd>
242 <dt><b>Angular</b></dt>
243 <dd>Remove center of mass translation and rotation around the center of mass
246 <dd>No restriction on the center of mass motion
248 <dt><b>nstcomm: (100) [steps]</b></dt>
249 <dd>frequency for center of mass motion removal</dd>
250 <dt><b>comm-grps:</b></dt>
251 <dd>group(s) for center of mass motion removal, default is the whole system</dd>
256 <h3><!--Idx-->Langevin dynamics<!--EIdx--></h3>
259 <dt><b>bd-fric: (0) [amu ps<sup>-1</sup>]</b></dt>
260 <dd>Brownian dynamics friction coefficient.
261 When <b>bd-fric</b><tt>=0</tt>, the friction coefficient for each
262 particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>.</dd>
263 <dt><b>ld-seed: (1993) [integer]</b></dt>
264 <dd>used to initialize random generator for thermal noise
265 for stochastic and Brownian dynamics.
266 When <b>ld-seed</b> is set to -1, the seed is calculated from the process ID.
267 When running BD or SD on multiple processors, each processor uses a seed equal
268 to <b>ld-seed</b> plus the processor number.</dd>
273 <h3>Energy minimization<!--QuietIdx-->energy minimization<!--EQuietIdx--></h3>
275 <dt><b>emtol: (10.0) [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
276 <dd>the minimization is converged when the maximum force is smaller than
278 <dt><b>emstep: (0.01) [nm]</b></dt>
279 <dd>initial step-size</dd>
280 <dt><b>nstcgsteep: (1000) [steps]</b></dt>
281 <dd>frequency of performing 1 steepest descent step while doing
282 conjugate gradient energy minimization.</dd>
283 <dt><b>nbfgscorr: (10)</b></dt>
284 <dd>Number of correction steps to use for L-BFGS minimization. A higher
285 number is (at least theoretically) more accurate, but slower.</dd>
288 <A NAME="shellmd"><br>
290 <h3>Shell Molecular Dynamics<!--QuietIdx-->shell molecular dynamics<!--EQuietIdx--></h3>
292 flexible constraints are present in the system the positions of the shells
293 and the lengths of the flexible constraints are optimized at
294 every time step until either the RMS force on the shells and constraints
295 is less than emtol, or a maximum number of iterations (niter) has been reached
297 <dt><b>emtol: (10.0) [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
298 <dd>the minimization is converged when the maximum force is smaller than
299 this value. For shell MD this value should be 1.0 at most, but since the
300 variable is used for energy minimization as well the default is 10.0.</dd>
301 <dt><b>niter: (20)</b></dt>
302 <dd>maximum number of iterations for optimizing the shell positions
303 and the flexible constraints.</dd>
304 <dt><b>fcstep: (0) [ps<sup>2</sup>]</b></dt>
305 <dd>the step size for optimizing the flexible constraints.
306 Should be chosen as mu/(d<sup>2</sup>V/dq<sup>2</sup>)
307 where mu is the reduced mass of two particles in a flexible constraint
308 and d<sup>2</sup>V/dq<sup>2</sup> is the second derivative of the potential
309 in the constraint direction. Hopefully this number does not differ too
310 much between the flexible constraints, as the number of iterations
311 and thus the runtime is very sensitive to <tt>fcstep</tt>.
312 Try several values!</dd>
317 <h3>Test particle insertion</h3>
319 <dt><b>rtpi: (0.05) [nm]</b></dt>
320 <dd>the test particle insertion radius see integrators
321 <b><a href="#run">tpi</a></b> and <b><a href="#run">tpic</a></b></dd>
326 <h3>Output control</h3>
328 <dt><b>nstxout: (0) [steps]</b></dt>
329 <dd>number of steps that elapse between writing coordinates to output
330 <!--Idx-->trajectory file<!--EIdx-->, the last coordinates are always written</dd>
331 <dt><b>nstvout: (0) [steps]</b></dt>
332 <dd>number of steps that elapse between writing velocities to output trajectory,
333 the last velocities are always written</dd>
334 <dt><b>nstfout: (0) [steps]</b></dt>
335 <dd>number of steps that elapse between writing forces to output trajectory.</dd>
336 <dt><b>nstlog: (1000) [steps]</b></dt>
337 <dd>number of steps that elapse between writing energies to the <!--Idx-->log file<!--EIdx-->,
338 the last energies are always written</dd>
339 <dt><b>nstcalcenergy: (100)</b></dt>
340 <dd>number of steps that elapse between calculating the energies, 0 is never.
341 This option is only relevant with dynamics.
342 With a twin-range cut-off setup <b>nstcalcenergy</b> should be equal to
343 or a multiple of <b>nstlist</b>.
344 This option affects the performance in parallel simulations,
345 because calculating energies requires global communication between all
346 processes which can become a bottleneck at high parallelization.
348 <dt><b>nstenergy: (1000) [steps]</b></dt>
349 <dd>number of steps that else between writing energies to energy file,
350 the last energies are always written,
351 should be a multiple of <b>nstcalcenergy</b>.
352 Note that the exact sums and fluctuations over all MD steps
353 modulo <b>nstcalcenergy</b> are stored in the energy file,
354 so <tt>g_energy</tt> can report exact
355 energy averages and fluctuations also when <b>nstenergy</b><tt>>1</tt></dd>
356 <dt><b>nstxout-compressed: (0) [steps]</b></dt>
357 <dd>number of steps that elapse between writing position coordinates using lossy compression</dd>
358 <dt><b>compressed-x-precision: (1000) [real]</b></dt>
359 <dd>precision with which to write to the compressed trajectory file</dd>
360 <dt><b>compressed-x-grps:</b></dt>
361 <dd>group(s) to write to the compressed trajectory file, by default the whole system is written
362 (if <b>nstxout-compressed</b> > 0)</dd>
363 <dt><b>energygrps:</b></dt>
364 <dd>group(s) to write to energy file</dd>
369 <h3>Neighbor searching<!--QuietIdx-->neighbor searching<!--EQuietIdx--></h3>
371 <dt><b>cutoff-scheme:</b></dt>
373 <dt><b>Verlet</b></dt>
374 <dd>Generate a pair list with buffering. The buffer size is automatically set
375 based on <b>verlet-buffer-tolerance</b>, unless this is set to -1, in which case
376 <b>rlist</b> will be used. This option has an explicit, exact cut-off at
377 <b>rvdw</b>=<b>rcoulomb</b>. Currently only cut-off, reaction-field,
378 PME electrostatics and plain LJ are supported. Some <tt>mdrun</tt> functionality
379 is not yet supported with the <b>Verlet</b> scheme, but <tt>grompp</tt> checks for this.
380 Native GPU acceleration is only supported with <b>Verlet</b>.
381 With GPU-accelerated PME or with separate PME ranks,
382 <tt>mdrun</tt> will automatically tune the CPU/GPU load balance by
383 scaling <b>rcoulomb</b> and the grid spacing. This can be turned off with
386 <b>Verlet</b> is faster than <b>group</b> when there is no water, or if <b>group</b> would use a pair-list buffer to conserve energy.
388 <dt><b>group</b></dt>
389 <dd>Generate a pair list for groups of atoms. These groups correspond to the
390 charge groups in the topology. This was the only cut-off treatment scheme
392 There is no explicit buffering of the pair list. This enables efficient force
393 calculations for water, but energy is only conserved when a buffer is explicitly added.</dd>
397 <dt><b>nstlist: (10) [steps]</b></dt>
399 <dt><b>>0</b></dt>
400 <dd>Frequency to update the <!--Idx-->neighbor list<!--EIdx--> (and
401 the long-range forces, when using twin-range cut-offs). When this is 0,
402 the neighbor list is made only once.
403 With energy minimization the neighborlist will be updated for every
404 energy evaluation when <b>nstlist</b><tt>>0</tt>.
405 With <b>cutoff-scheme=Verlet</b> and <b>verlet-buffer-tolerance</b> set,
406 <b>nstlist</b> is actually a minimum value and <tt>mdrun</tt> might increase it.
407 With parallel simulations and/or non-bonded force calculation on the GPU,
408 a value of 20 or 40 often gives the best performance.
409 With <b>cutoff-scheme=Group</b> and non-exact cut-off's, <b>nstlist</b> will
410 affect the accuracy of your simulation and it can not be chosen freely.
413 <dd>The neighbor list is only constructed once and never updated.
414 This is mainly useful for vacuum simulations in which all particles
417 <dd>Automated update frequency, only supported with <b>cutoff-scheme</b>=<b>group</b>.
418 This can only be used with switched, shifted or user potentials where
419 the cut-off can be smaller than <b>rlist</b>. One then has a buffer
420 of size <b>rlist</b> minus the longest cut-off.
421 The neighbor list is only updated when one or more particles have moved further
422 than half the buffer size from the center of geometry of their charge group
423 as determined at the previous neighbor search.
424 Coordinate scaling due to pressure coupling or the <b>deform</b> option
425 is taken into account.
426 This option guarantees that their are no cut-off artifacts,
427 but for larger systems this can come at a high computational cost,
428 since the neighbor list update frequency will be determined
429 by just one or two particles moving slightly beyond the half buffer length
430 (which does not necessarily imply that the neighbor list is invalid),
431 while 99.99% of the particles are fine.
435 <dt><b>nstcalclr: (-1) [steps]</b></dt>
437 Controls the period between calculations of long-range forces when
438 using the group cut-off scheme.
441 <dd>Calculate the long-range forces every single step. This is useful
442 to have separate neighbor lists with buffers for electrostatics and Van
443 der Waals interactions, and in particular it makes it possible to have
444 the Van der Waals cutoff longer than electrostatics (useful e.g. with
445 PME). However, there is no point in having identical long-range
446 cutoffs for both interaction forms and update them every step - then
447 it will be slightly faster to put everything in the short-range
449 <dt><b>>1</b></dt>
450 <dd>Calculate the long-range forces every <b>nstcalclr</b> steps and
451 use a multiple-time-step integrator to combine forces. This can now be
452 done more frequently than <b>nstlist</b> since the lists are stored,
453 and it might be a good idea e.g. for Van der Waals interactions that
454 vary slower than electrostatics.</dd>
456 <dd>Calculate long-range forces on steps where neighbor searching is
457 performed. While this is the default value, you might want to consider
458 updating the long-range forces more frequently.</dd>
460 Note that twin-range force evaluation might be enabled automatically
461 by PP-PME load balancing. This is done in order to maintain the chosen
462 Van der Waals interaction radius even if the load balancing is
463 changing the electrostatics cutoff. If the <tt>.mdp</tt> file already
464 specifies twin-range interactions (e.g. to evaluate Lennard-Jones
465 interactions with a longer cutoff than the PME electrostatics every
466 2-3 steps), the load balancing will have also a small effect on
467 Lennard-Jones, since the short-range cutoff (inside which forces are
468 evaluated every step) is changed.
473 <dt><b>ns-type:</b></dt>
476 <dd>Make a grid in the box and only check atoms in neighboring grid
477 cells when constructing a new neighbor list every <b>nstlist</b> steps.
478 In large systems grid search is much faster than simple search.</dd>
479 <dt><b>simple</b></dt>
480 <dd>Check every atom in the box when constructing a new neighbor list
481 every <b>nstlist</b> steps (only with <b>cutoff-scheme=group</b>).</dd>
487 <dd>Use periodic boundary conditions in all directions.</dd>
489 <dd>Use no periodic boundary conditions, ignore the box.
490 To simulate without cut-offs, set all cut-offs to 0 and <b>nstlist</b><tt>=0</tt>.
491 For best performance without cut-offs, use <b>nstlist</b><tt>=0</tt>,
492 <b>ns-type</b><tt>=simple</tt>
493 and particle decomposition instead of domain decomposition.</dd>
495 <dd>Use periodic boundary conditions in x and y directions only.
496 This works only with <b>ns-type</b><tt>=grid</tt> and can be used
497 in combination with <b><a href="#walls">walls</a></b>.
498 Without walls or with only one wall the system size is infinite
499 in the z direction. Therefore pressure coupling or Ewald summation
500 methods can not be used.
501 These disadvantages do not apply when two walls are used.</dd>
504 <dt><b>periodic-molecules:</b></dt>
507 <dd>molecules are finite, fast molecular PBC can be used</dd>
509 <dd>for systems with molecules that couple to themselves through
510 the periodic boundary conditions, this requires a slower PBC algorithm
511 and molecules are not made whole in the output</dd>
514 <dt><b>verlet-buffer-tolerance: (0.005) [kJ/mol/ps]</b></dt>
515 <dd>Useful only with <b>cutoff-scheme</b>=<b>Verlet</b>. This sets the maximum
516 allowed error for pair interactions per particle caused by the Verlet buffer,
517 which indirectly sets <b>rlist</b>.
518 As both <b>nstlist</b> and the Verlet buffer size are fixed
519 (for performance reasons), particle pairs not in the pair list can occasionally
520 get within the cut-off distance during <b>nstlist</b>-1 nsteps. This
521 causes very small jumps in the energy. In a constant-temperature ensemble,
522 these very small energy jumps can be
523 estimated for a given cut-off and <b>rlist</b>. The estimate assumes a
524 homogeneous particle distribution, hence the errors might be slightly
525 underestimated for multi-phase systems. For longer pair-list life-time
526 (<b>nstlist</b>-1)*dt the buffer is overestimated, because the interactions
527 between particles are ignored. Combined with cancellation of errors,
528 the actual drift of the total energy is usually one to two orders of magnitude
530 Note that the generated buffer size takes into account that
531 the GROMACS pair-list setup leads to a reduction in the drift by
532 a factor 10, compared to a simple particle-pair based list.
533 Without dynamics (energy minimization etc.), the buffer is 5% of the cut-off.
534 For NVE simulations the initial temperature is used, unless this is zero,
535 in which case a buffer of 10% is used. For NVE simulations the tolerance
536 usually needs to be lowered to achieve proper energy conservation on
537 the nanosecond time scale. To override the automated buffer setting,
538 use <b>verlet-buffer-tolerance</b>=-1 and set <b>rlist</b> manually.</dd>
540 <dt><b>rlist: (1) [nm]</b></dt>
541 <dd>Cut-off distance for the short-range neighbor list.
542 With <b>cutoff-scheme</b>=<b>Verlet</b>, this is by default set by the
543 <b>verlet-buffer-tolerance</b> option and the value of <b>rlist</b> is ignored.</dd>
545 <dt><b>rlistlong: (-1) [nm]</b></dt>
546 <dd>Cut-off distance for the long-range neighbor list.
547 This parameter is only relevant for a twin-range cut-off setup
548 with switched potentials. In that case a buffer region is required to account
549 for the size of charge groups. In all other cases this parameter
550 is automatically set to the longest cut-off distance.</dd>
556 <h3>Electrostatics<!--QuietIdx-->electrostatics<!--EQuietIdx--></h3>
558 <dt><b>coulombtype:</b></dt>
561 <dt><b>Cut-off</b></dt>
562 <dd>Twin range cut-offs with neighborlist cut-off <b>rlist</b> and
563 Coulomb cut-off <b>rcoulomb</b>,
564 where <b>rcoulomb</b>≥<b>rlist</b>.
566 <dt><b>Ewald</b></dt>
567 <dd>Classical <!--Idx-->Ewald sum<!--EIdx--> electrostatics.
568 The real-space cut-off <b>rcoulomb</b> should be equal to <b>rlist</b>.
569 Use e.g. <b>rlist</b><tt>=0.9</tt>, <b>rcoulomb</b><tt>=0.9</tt>. The highest magnitude of
570 wave vectors used in reciprocal space is controlled by <b>fourierspacing</b>.
571 The relative accuracy of direct/reciprocal space
572 is controlled by <b>ewald-rtol</b>.
574 NOTE: Ewald scales as O(N<sup>3/2</sup>)
575 and is thus extremely slow for large systems. It is included mainly for
576 reference - in most cases PME will perform much better.</dd>
578 <dt><b><!--Idx-->PME<!--EIdx--></b></dt>
579 <dd>Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct space is similar
580 to the Ewald sum, while the reciprocal part is performed with
581 FFTs. Grid dimensions are controlled with <b>fourierspacing</b> and the
582 interpolation order with <b>pme-order</b>. With a grid spacing of 0.1
583 nm and cubic interpolation the electrostatic forces have an accuracy
584 of 2-3*10<sup>-4</sup>. Since the error from the vdw-cutoff is larger than this you
585 might try 0.15 nm. When running in parallel the interpolation
586 parallelizes better than the FFT, so try decreasing grid dimensions
587 while increasing interpolation.</dd>
589 <dt><b><!--Idx-->P3M-AD<!--EIdx--></b></dt>
590 <dd>Particle-Particle Particle-Mesh algorithm with analytical derivative
591 for for long range electrostatic interactions. The method and code
592 is identical to SPME, except that the influence function is optimized
593 for the grid. This gives a slight increase in accuracy.</dd>
595 <dt><b>Reaction-Field electrostatics<!--QuietIdx-->reaction-field electrostatics<!--EQuietIdx--></b></dt>
596 <dd>Reaction field with Coulomb cut-off <b>rcoulomb</b>,
597 where <b>rcoulomb</b> ≥ <b>rlist</b>.
598 The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
599 The dielectric constant can be set to infinity by setting <b>epsilon-rf</b><tt>=0</tt>.</dd>
601 <dt><b>Generalized-Reaction-Field</b></dt>
602 <dd>Generalized reaction field with Coulomb cut-off <b>rcoulomb</b>,
603 where <b>rcoulomb</b> ≥ <b>rlist</b>.
604 The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
605 The ionic strength is computed from the number of charged
606 (i.e. with non zero charge) <!--Idx-->charge group<!--EIdx-->s.
607 The temperature for the GRF potential is set with
608 <b><A HREF="#tc">ref-t</A></b> [K].</dd>
610 <dt><b>Reaction-Field-zero</b></dt>
611 <dd>In GROMACS, normal reaction-field electrostatics with
612 <b>cutoff-scheme</b><b>=group</b> leads to bad
613 energy conservation. <b>Reaction-Field-zero</b> solves this
614 by making the potential zero beyond the cut-off. It can only
615 be used with an infinite dielectric constant (<b>epsilon-rf=0</b>),
616 because only for that value the force vanishes at the cut-off.
617 <b>rlist</b> should be 0.1 to 0.3 nm larger than <b>rcoulomb</b>
618 to accommodate for the size of charge groups and diffusion
619 between neighbor list updates. This, and the fact that table lookups
620 are used instead of analytical functions make <b>Reaction-Field-zero</b>
621 computationally more expensive than normal reaction-field.</dd>
623 <dt><b>Reaction-Field-nec</b></dt>
624 <dd>The same as <b>Reaction-Field</b>, but implemented as in
625 GROMACS versions before 3.3. No reaction-field correction is applied
626 to excluded atom pairs and self pairs.
627 The 1-4 interactions are calculated using a reaction-field.
628 The missing correction due to the excluded pairs that do not have a 1-4
629 interaction is up to a few percent of the total electrostatic
630 energy and causes a minor difference in the forces and the pressure.</dd>
632 <dt><b>Shift</b></dt>
633 <dd>Analogous to <b>Shift</b> for <b>vdwtype</b>.
634 You might want to use <b>Reaction-Field-zero</b> instead,
635 which has a similar potential shape, but has a physical interpretation
636 and has better energies due to the exclusion correction terms.
639 <dt><b>Encad-Shift</b></dt>
641 potential is decreased over the whole range, using the definition
642 from the Encad simulation package.</dd>
644 <dt><b>Switch</b></dt>
645 <dd>Analogous to <b>Switch</b> for <b>vdwtype</b>.
646 Switching the Coulomb potential can lead to serious artifacts,
647 advice: use <b>Reaction-Field-zero</b> instead.</dd>
650 <dd><a name="usertab"></a><tt>mdrun</tt> will now expect to find a file
651 <tt>table.xvg</tt> with user-defined potential functions for
652 repulsion, dispersion and Coulomb. When pair interactions are present,
653 <tt>mdrun</tt> also expects to find a file <tt>tablep.xvg</tt> for
654 the pair interactions. When the same interactions should be used
655 for non-bonded and pair interactions the user can specify the same
656 file name for both table files.
657 These files should contain 7
658 columns: the <tt>x</tt> value,
659 <tt>f(x)</tt>, <tt>-f'(x)</tt>,
660 <tt>g(x)</tt>, <tt>-g'(x)</tt>,
661 <tt>h(x)</tt>, <tt>-h'(x)</tt>,
662 where <tt>f(x)</tt> is the Coulomb function, <tt>g(x)</tt> the dispersion function
663 and <tt>h(x)</tt> the repulsion function.
664 When <b>vdwtype</b> is not set to <b>User</b> the values
665 for <tt>g</tt>, <tt>-g'</tt>, <tt>h</tt> and <tt>-h'</tt> are ignored.
666 For the non-bonded interactions <tt>x</tt> values should run
667 from 0 to the largest cut-off distance + <b>table-extension</b>
668 and should be uniformly spaced. For the pair interactions the table
669 length in the file will be used.
670 The optimal spacing, which is used for non-user tables,
671 is <tt>0.002</tt> [nm] when you run in single precision
672 or <tt>0.0005</tt> [nm] when you run in double precision.
673 The function value at <tt>x=0</tt> is not important. More information is
674 in the printed manual.</dd>
676 <dt><b>PME-Switch</b></dt>
677 <dd>A combination of PME and a switch function for the direct-space part
678 (see above). <b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
679 This is mainly useful constant energy simulations (note that using
680 <b>PME</b> with <b>cutoff-scheme</b>=<b>Verlet</b> will be more efficient).
683 <dt><b>PME-User</b></dt>
684 <dd>A combination of PME and user tables (see above).
685 <b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
686 The PME mesh contribution is subtracted from the user table by <tt>mdrun</tt>.
687 Because of this subtraction the user tables should contain
688 about 10 decimal places.</dd>
690 <dt><b>PME-User-Switch</b></dt>
691 <dd>A combination of PME-User and a switching function (see above).
692 The switching function is applied to final particle-particle interaction,
693 i.e. both to the user supplied function and the PME Mesh correction part.</dd>
697 <dt><b>coulomb-modifier:</b></dt>
699 <dt><b>Potential-shift-Verlet</b></dt>
700 <dd>Selects <b>Potential-shift</b> with the Verlet cutoff-scheme,
701 as it is (nearly) free; selects <b>None</b> with the group cutoff-scheme.</dd>
702 <dt><b>Potential-shift</b></dt>
703 <dd>Shift the Coulomb potential by a constant such that it is zero at the cut-off.
704 This makes the potential the integral of the force. Note that this does not
705 affect the forces or the sampling.</dd>
707 <dd>Use an unmodified Coulomb potential. With the group scheme this means no exact cut-off is used, energies and forces are calculated for all pairs in the neighborlist.</dd>
712 <dt><b>rcoulomb-switch: (0) [nm]</b></dt>
713 <dd>where to start switching the Coulomb potential</dd>
715 <dt><b>rcoulomb: (1) [nm]</b></dt>
716 <dd>distance for the Coulomb <!--Idx-->cut-off<!--EIdx--></dd>
718 <dt><b>epsilon-r: (1)</b></dt>
719 <dd>The relative <!--Idx-->dielectric constant<!--EIdx-->.
720 A value of 0 means infinity.</dd>
722 <dt><b>epsilon-rf: (0)</b></dt>
723 <dd>The relative dielectric constant of the reaction field.
724 This is only used with reaction-field electrostatics.
725 A value of 0 means infinity.</dd>
732 <dt><b>vdwtype:</b></dt>
734 <dt><b>Cut-off</b></dt>
735 <dd>Twin range cut-offs with neighbor list cut-off <b>rlist</b> and
736 VdW cut-off <b>rvdw</b>,
737 where <b>rvdw</b> <tt>≥</tt> <b>rlist</b>.</dd>
740 <dd>Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
741 grid dimensions are controlled with <b>fourierspacing</b> in the same
742 way as for electrostatics, and the interpolation order is controlled
743 with <b>pme-order</b>. The relative accuracy of direct/reciprocal
744 space is controlled by <b>ewald-rtol-lj</b>, and the specific
745 combination rules that are to be used by the reciprocal routine are
746 set using <b>lj-pme-comb-rule</b>.</dd>
748 <dt><b>Shift</b></dt>
749 <dd>The LJ (not Buckingham) potential is decreased over the whole
750 range and the forces decay smoothly to zero between <b>rvdw-switch</b>
751 and <b>rvdw</b>. The neighbor search cut-off <b>rlist</b> should be
752 0.1 to 0.3 nm larger than <b>rvdw</b> to accommodate for the size of
753 charge groups and diffusion between neighbor list
756 <dt><b>Switch</b></dt>
757 <dd>The LJ (not Buckingham)
758 potential is normal out to <b>rvdw-switch</b>, after which it is switched
759 off to reach zero at <b>rvdw</b>. Both the potential and force functions
760 are continuously smooth, but be aware that all switch functions will give rise
761 to a bulge (increase) in the force (since we are switching the potential).
762 The neighbor search cut-off <b>rlist</b> should be 0.1 to 0.3 nm larger than
763 <b>rvdw</b> to accommodate for the size of charge groups and diffusion
764 between neighbor list updates.</dd>
766 <dt><b>Encad-Shift</b></dt>
767 <dd>The LJ (not Buckingham)
768 potential is decreased over the whole range, using the definition
769 from the Encad simulation package.</dd>
772 <dd>See <b><a href="#usertab">user</a></b> for <b>coulombtype</b>.
773 The function value at <tt>x=0</tt> is not important. When you want to
774 use LJ correction, make sure that <b>rvdw</b> corresponds to the
775 cut-off in the user-defined function.
776 When <b>coulombtype</b> is not set to <b>User</b> the values
777 for <tt>f</tt> and <tt>-f'</tt> are ignored.</dd>
780 <dt><b>vdw-modifier:</b></dt>
782 <dt><b>Potential-shift-Verlet</b></dt>
783 <dd>Selects <b>Potential-shift</b> with the Verlet cutoff-scheme,
784 as it is (nearly) free; selects <b>None</b> with the group cutoff-scheme.</dd>
785 <dt><b>Potential-shift</b></dt>
786 <dd>Shift the Van der Waals potential by a constant such that it is zero at the cut-off.
787 This makes the potential the integral of the force. Note that this does not
788 affect the forces or the sampling.</dd>
790 <dd>Use an unmodified Van der Waals potential. With the group scheme this means no exact cut-off is used, energies and forces are calculated for all pairs in the neighborlist.</dd>
793 <dt><b>rvdw-switch: (0) [nm]</b></dt>
794 <dd>where to start switching the LJ potential</dd>
796 <dt><b>rvdw: (1) [nm]</b></dt>
797 <dd>distance for the LJ or Buckingham <!--Idx-->cut-off<!--EIdx--></dd>
799 <dt><b>DispCorr:</b></dt>
800 <dd><dl compact></dd>
802 <dd>don't apply any correction</dd>
803 <dt><b>EnerPres</b></dt>
804 <dd>apply long range <!--Idx-->dispersion correction<!--EIdx-->s for Energy
807 <dd>apply long range dispersion corrections for Energy
816 <dt><b>table-extension: (1) [nm]</b></dt>
817 <dd>Extension of the non-bonded potential lookup tables beyond the largest cut-off distance.
818 The value should be large enough to account for charge group sizes
819 and the diffusion between neighbor-list updates.
820 Without user defined potential the same table length is used
821 for the lookup tables for the 1-4 interactions,
822 which are always tabulated irrespective of the use of
823 tables for the non-bonded interactions. The value of <b>table-extension</b> in no way
824 affects the values of <b>rlist</b>, <b>rcoulomb</b>, or <b>rvdw</b>. </dd>
826 <dt><b>energygrp-table:</b></dt>
827 <dd>When user tables are used for electrostatics and/or VdW,
828 here one can give pairs of energy groups for which seperate
829 user tables should be used.
830 The two energy groups will be appended to the table file name,
831 in order of their definition in <b>energygrps</b>, seperated by underscores.
832 For example, if <tt>energygrps = Na Cl Sol</tt>
833 and <tt>energygrp-table = Na Na Na Cl</tt>, <tt>mdrun</tt> will read
834 <tt>table_Na_Na.xvg</tt> and <tt>table_Na_Cl.xvg</tt> in addition
835 to the normal <tt>table.xvg</tt> which will be used for all other
844 <dt><b>fourierspacing: (0.12) [nm]</b></dt>
845 <dd>For ordinary Ewald, the ratio of the box dimensions and the spacing
846 determines a lower bound for the number of wave vectors to use in each
847 (signed) direction. For PME and P3M, that ratio determines a lower bound
848 for the number of Fourier-space grid points that will be used along that
849 axis. In all cases, the number for each direction can be overridden by
850 entering a non-zero value for <b>fourier_n[xyz]</b>.
851 For optimizing the relative load of the particle-particle interactions
852 and the mesh part of PME, it is useful to know that
853 the accuracy of the electrostatics remains nearly constant
854 when the Coulomb cut-off and the PME grid spacing are scaled
855 by the same factor.</dd>
857 <dt><b>fourier-nx (0) ; fourier-ny (0) ; fourier-nz: (0)</b></dt>
858 <dd>Highest magnitude of wave vectors in reciprocal space when using Ewald.</dd>
859 <dd>Grid size when using PME or P3M. These values override
860 <b>fourierspacing</b> per direction. The best choice is powers of
861 2, 3, 5 and 7. Avoid large primes.</dd>
863 <dt><b>pme-order (4)</b></dt>
864 <dd>Interpolation order for PME. 4 equals cubic interpolation. You might try
865 6/8/10 when running in parallel and simultaneously decrease grid dimension.</dd>
867 <dt><b>ewald-rtol (1e-5)</b></dt>
868 <dd>The relative strength of the Ewald-shifted direct potential at
869 <b>rcoulomb</b> is given by <b>ewald-rtol</b>.
870 Decreasing this will give a more accurate direct sum,
871 but then you need more wave vectors for the reciprocal sum.</dd>
873 <dt><b>ewald-rtol-lj (1e-3)</b></dt>
874 <dd>When doing PME for VdW-interactions, <b>ewald-rtol-lj</b> is used
875 to control the relative strength of the dispersion potential at <b>rvdw</b> in
876 the same way as <b>ewald-rtol</b> controls the electrostatic potential.</dd>
878 <dt><b>lj-pme-comb-rule (Geometric)</b></dt>
879 <dd>The combination rules used to combine VdW-parameters in the reciprocal part of LJ-PME.
880 Geometric rules are much faster than Lorentz-Berthelot and usually the recommended choice, even
881 when the rest of the force field uses the Lorentz-Berthelot rules.</dd>
883 <dt><b>Geometric</b></dt>
884 <dd>Apply geometric combination rules</dd>
885 <dt><b>Lorentz-Berthelot</b></dt>
886 <dd>Apply Lorentz-Berthelot combination rules</dd>
889 <dt><b>ewald-geometry: (3d)</b></dt>
892 <dd>The Ewald sum is performed in all three dimensions.</dd>
894 <dd>The reciprocal sum is still performed in 3D,
895 but a force and potential correction applied in the <tt>z</tt>
896 dimension to produce a pseudo-2D summation.
897 If your system has a slab geometry in the <tt>x-y</tt> plane you can
898 try to increase the <tt>z</tt>-dimension of the box (a box height of 3 times
899 the slab height is usually ok)
900 and use this option.</dd>
903 <dt><b>epsilon-surface: (0)</b></dt>
904 <dd>This controls the dipole correction to the Ewald summation in 3D. The
905 default value of zero means it is turned off. Turn it on by setting it to the value
906 of the relative permittivity of the imaginary surface around your infinite system. Be
907 careful - you shouldn't use this if you have free mobile charges in your system.
908 This value does not affect the slab 3DC variant of the long range corrections.</dd>
911 <dt><b>optimize-fft:</b></dt>
914 <dd>Don't calculate the optimal FFT plan for the grid at startup.</dd>
916 <dd>Calculate the optimal FFT plan for the grid at startup. This saves a
917 few percent for long simulations, but takes a couple of minutes
925 <h3>Temperature coupling<!--QuietIdx-->temperature coupling<!--EQuietIdx--></h3>
928 <dt><b>tcoupl:</b></dt>
931 <dd>No temperature coupling.</dd>
932 <dt><b>berendsen</b></dt>
933 <dd>Temperature coupling with a Berendsen-thermostat to a bath with
934 temperature <b>ref-t</b> [K], with time constant <b>tau-t</b> [ps].
935 Several groups can be coupled separately, these are specified in the
936 <b>tc-grps</b> field separated by spaces.</dd>
937 <dt><b>nose-hoover</b></dt>
938 <dd>Temperature coupling using a Nose-Hoover extended
939 ensemble. The reference temperature and coupling groups are selected
940 as above, but in this case <b>tau-t</b> [ps] controls the period
941 of the temperature fluctuations at equilibrium, which is slightly
942 different from a relaxation time.
943 For NVT simulations the conserved energy quantity is written
944 to energy and log file.</dd>
945 <dt><b>v-rescale</b></dt>
946 <dd>Temperature coupling using velocity rescaling with a stochastic term
948 This thermostat is similar to Berendsen coupling, with the same scaling
949 using <b>tau-t</b>, but the stochastic term ensures that a proper
950 canonical ensemble is generated. The random seed is set with
951 <b><A HREF="#ld">ld-seed</A></b>.
952 This thermostat works correctly even for <b>tau-t</b><tt>=0</tt>.
953 For NVT simulations the conserved energy quantity is written
954 to the energy and log file.</dd>
956 <dt><b>nsttcouple: (-1)</b></dt>
957 <dd>The frequency for coupling the temperature.
958 The default value of -1 sets <b>nsttcouple</b> equal to <b>nstlist</b>,
959 unless <b>nstlist</b>≤0, then a value of 10 is used.
960 For velocity Verlet integrators <b>nsttcouple</b> is set to 1.</dd>
962 <dt><b>nh-chain-length (10)</b></dt>
963 <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>
964 <dt><b>tc-grps:</b></dt>
965 <dd>groups to couple separately to temperature bath</dd>
966 <dt><b>tau-t: [ps]</b></dt>
967 <dd>time constant for coupling (one for each group in <b>tc-grps</b>),
968 -1 means no temperature coupling</dd>
969 <dt><b>ref-t: [K]</b></dt>
970 <dd>reference temperature for coupling (one for each group in <b>tc-grps</b>)</dd>
975 <h3>Pressure coupling<!--QuietIdx-->pressure coupling<!--EQuietIdx--></h3>
978 <dt><b>pcoupl:</b></dt>
981 <dd>No pressure coupling. This means a fixed box size.</dd>
982 <dt><b>berendsen</b></dt>
983 <dd>Exponential relaxation pressure coupling with time constant
984 <b>tau-p</b> [ps]. The box is scaled every timestep. It has been
985 argued that this does not yield a correct thermodynamic ensemble,
986 but it is the most efficient way to scale a box at the beginning
988 <dt><b>Parrinello-Rahman</b></dt>
989 <dd>Extended-ensemble pressure coupling where the box vectors are
990 subject to an equation of motion. The equation of motion for the atoms
991 is coupled to this. No instantaneous scaling takes place. As for
992 Nose-Hoover temperature coupling the time constant <b>tau-p</b> [ps]
993 is the period of pressure fluctuations at equilibrium. This is
994 probably a better method when you want to apply pressure scaling
995 during data collection, but beware that you can get very large
996 oscillations if you are starting from a different pressure. For
997 simulations where the exact fluctation of the NPT ensemble are
998 important, or if the pressure coupling time is very short it may not
999 be appropriate, as the previous time step pressure is used in some
1000 steps of the GROMACS implementation for the current time step pressure.</dd>
1002 <dt><b>MTTK</b></dt>
1003 <dd>Martyna-Tuckerman-Tobias-Klein implementation, only useable with <b>md-vv</b>
1004 or <b>md-vv-avek</b>, very similar to Parrinello-Rahman.
1005 As for Nose-Hoover temperature coupling the time constant <b>tau-p</b>
1006 [ps] is the period of pressure fluctuations at equilibrium. This is
1007 probably a better method when you want to apply pressure scaling
1008 during data collection, but beware that you can get very large
1009 oscillations if you are starting from a different pressure. Currently only supports isotropic scaling.</dd>
1013 <dt><b>pcoupltype:</b></dt>
1015 <dt><b>isotropic</b></dt>
1016 <dd>Isotropic pressure coupling with time constant <b>tau-p</b> [ps].
1017 The compressibility and reference pressure are set with
1018 <b>compressibility</b> [bar<sup>-1</sup>] and <b>ref-p</b> [bar], one
1019 value is needed.</dd>
1020 <dt><b>semiisotropic</b></dt>
1021 <dd>Pressure coupling which is isotropic in the <tt>x</tt> and <tt>y</tt> direction,
1022 but different in the <tt>z</tt> direction.
1023 This can be useful for membrane simulations.
1024 2 values are needed for <tt>x/y</tt> and <tt>z</tt> directions respectively.</dd>
1025 <dt><b>anisotropic</b></dt>
1026 <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>
1027 components, respectively.
1028 When the off-diagonal compressibilities are set to zero,
1029 a rectangular box will stay rectangular.
1030 Beware that anisotropic scaling can lead to extreme deformation
1031 of the simulation box.</dd>
1032 <dt><b>surface-tension</b></dt>
1033 <dd>Surface tension coupling for surfaces parallel to the xy-plane.
1034 Uses normal pressure coupling for the <tt>z</tt>-direction, while the surface tension
1035 is coupled to the <tt>x/y</tt> dimensions of the box.
1036 The first <b>ref-p</b> value is the reference surface tension times
1037 the number of surfaces [bar nm],
1038 the second value is the reference <tt>z</tt>-pressure [bar].
1039 The two <b>compressibility</b> [bar<sup>-1</sup>] values are the compressibility
1040 in the <tt>x/y</tt> and <tt>z</tt> direction respectively.
1041 The value for the <tt>z</tt>-compressibility should be reasonably accurate since it
1042 influences the convergence of the surface-tension, it can also be set to zero
1043 to have a box with constant height.</dd>
1046 <dt><b>nstpcouple: (-1)</b></dt>
1047 <dd>The frequency for coupling the pressure.
1048 The default value of -1 sets <b>nstpcouple</b> equal to <b>nstlist</b>,
1049 unless <b>nstlist</b> ≤0, then a value of 10 is used.
1050 For velocity Verlet integrators <b>nstpcouple</b> is set to 1.</dd>
1053 <dt><b>tau-p: (1) [ps]</b></dt>
1054 <dd>time constant for coupling</dd>
1055 <dt><b>compressibility: [bar<sup>-1</sup>]</b></dt>
1056 <dd>compressibility (NOTE: this is now really in bar<sup>-1</sup>)
1057 For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar<sup>-1</sup>].</dd>
1058 <dt><b>ref-p: [bar]</b></dt>
1059 <dd>reference pressure for coupling</dd>
1060 <dt><b>refcoord-scaling:</b></dt>
1063 <dd>The reference coordinates for position restraints are not modified.
1064 Note that with this option the virial and pressure will depend on the absolute
1065 positions of the reference coordinates.</dd>
1067 <dd>The reference coordinates are scaled with the scaling matrix of the pressure coupling.</dd>
1069 <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.
1076 <h3>Simulated annealing<!--QuietIdx-->simulated annealing<!--EQuietIdx--></h3>
1078 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!
1080 <dt><b>annealing:</b></dt>
1081 <dd>Type of annealing for each temperature group</dd>
1082 <dd><dl compact></dd>
1084 <dd>No simulated annealing - just couple to reference temperature value.</dd>
1085 <dt><b>single</b></dt>
1086 <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>
1087 <dt><b>periodic</b></dt>
1088 <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.
1092 <dt><b>annealing-npoints:</b></dt>
1093 <dd>A list with the number of annealing reference/control points used for
1094 each temperature group. Use 0 for groups that are not annealed. The number of entries should equal the number of temperature groups.</dd>
1096 <dt><b>annealing-time:</b></dt>
1097 <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>
1099 <dt><b>annealing-temp:</b></dt>
1100 <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>
1102 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>.
1103 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!
1108 <h3>Velocity generation</h3>
1111 <dt><b>gen-vel:</b></dt>
1114 <dd> Do not generate velocities. The velocities are set to zero
1115 when there are no velocities in the input structure file.</dd>
1117 <dd>Generate velocities in <tt>grompp</tt> according to a Maxwell distribution at
1118 temperature <b>gen-temp</b> [K], with random seed <b>gen-seed</b>.
1119 This is only meaningful with integrator <b><A HREF="#run">md</A></b>.</dd>
1121 <dt><b>gen-temp: (300) [K]</b></dt>
1122 <dd>temperature for Maxwell distribution</dd>
1123 <dt><b>gen-seed: (173529) [integer]</b></dt>
1124 <dd>used to initialize random generator for random velocities,
1125 when <b>gen-seed</b> is set to -1, the seed is calculated from
1126 the process ID number.
1134 <dt><b>constraints<!--QuietIdx-->constraint algorithms<!--EQuietIdx-->:</b></dt>
1136 <dt><b>none</b></dt>
1137 <dd>No constraints except for those defined explicitly in the topology,
1138 i.e. bonds are represented by a harmonic (or other) potential
1139 or a Morse potential (depending on the setting of <b>morse</b>)
1140 and angles by a harmonic (or other) potential.
1141 <dt><b>h-bonds</b></dt>
1142 <dd>Convert the bonds with H-atoms to constraints.</dd>
1143 <dt><b>all-bonds</b></dt>
1144 <dd>Convert all bonds to constraints.</dd>
1145 <dt><b>h-angles</b></dt>
1146 <dd>Convert all bonds and additionally the angles that involve H-atoms
1147 to bond-constraints.</dd>
1148 <dt><b>all-angles</b></dt>
1149 <dd>Convert all bonds and angles to bond-constraints.</dd>
1152 <dt><b>constraint-algorithm:</b></dt>
1154 <dt><b><!--Idx-->LINCS<!--EIdx--></b></dt>
1155 <dd>LINear Constraint Solver.
1156 With domain decomposition the parallel version P-LINCS is used.
1157 The accuracy in set with
1158 <b>lincs-order</b>, which sets the number of matrices in the expansion
1159 for the matrix inversion.
1160 After the matrix inversion correction the algorithm does
1161 an iterative correction to compensate for lengthening due to rotation.
1162 The number of such iterations can be controlled with
1163 <b>lincs-iter</b>. The root mean square relative constraint deviation
1164 is printed to the log file every <b>nstlog</b> steps.
1165 If a bond rotates more than <b>lincs-warnangle</b> [degrees] in one step,
1166 a warning will be printed both to the log file and to <TT>stderr</TT>.
1167 LINCS should not be used with coupled angle constraints.
1169 <dt><b><!--Idx-->SHAKE<!--EIdx--></b></dt>
1170 <dd>SHAKE is slightly slower and less stable than LINCS, but does work with
1172 The relative tolerance is set with <b>shake-tol</b>, 0.0001 is a good value
1173 for ``normal'' MD. SHAKE does not support constraints between atoms
1174 on different nodes, thus it can not be used with domain decompositon
1175 when inter charge-group constraints are present.
1176 SHAKE can not be used with energy minimization.
1179 <dt><b>continuation:</b></dt>
1180 <dd>This option was formerly known as <tt>unconstrained-start</tt>.</dd>
1183 <dd>apply constraints to the start configuration and reset shells</dd>
1185 <dd>do not apply constraints to the start configuration
1186 and do not reset shells, useful for exact coninuation and reruns</dd>
1190 <dt><b>shake-tol: (0.0001)</b></dt>
1191 <dd>relative tolerance for SHAKE</dd>
1192 <dt><b>lincs-order: (4)</b></dt>
1193 <dd>Highest order in the expansion of the constraint coupling matrix.
1194 When constraints form triangles, an additional expansion of the same
1195 order is applied on top of the normal expansion only for the couplings
1196 within such triangles.
1197 For ``normal'' MD simulations an order of 4 usually suffices, 6 is
1198 needed for large time-steps with virtual sites or BD.
1199 For accurate energy minimization an order of 8 or more might be required.
1200 With domain decomposition, the cell size is limited by the distance
1201 spanned by <b>lincs-order</b>+1 constraints. When one wants to scale
1202 further than this limit, one can decrease <b>lincs-order</b> and increase
1203 <b>lincs-iter</b>, since the accuracy does not deteriorate
1204 when (1+<b>lincs-iter</b>)*<b>lincs-order</b> remains constant.</dd>
1205 <dt><b>lincs-iter: (1)</b></dt>
1206 <dd>Number of iterations to correct for rotational lengthening in LINCS.
1207 For normal runs a single step is sufficient, but for NVE
1208 runs where you want to conserve energy accurately or for accurate
1209 energy minimization you might want to increase it to 2.
1210 <dt><b>lincs-warnangle: </b>(30) [degrees]</dt>
1211 <dd>maximum angle that a bond can rotate before LINCS will complain</dd>
1213 <dt><b>morse:</b></dt>
1216 <dd>bonds are represented by a harmonic potential</dd>
1218 <dd>bonds are represented by a Morse potential</dd>
1222 <A NAME="egexcl"><br>
1224 <h3>Energy group <!--Idx-->exclusions<!--EIdx--></h3>
1226 <dt><b>energygrp-excl: </b></dt>
1227 <dd>Pairs of energy groups for which all non-bonded interactions are
1228 excluded. An example: if you have two energy groups <tt>Protein</tt>
1229 and <tt>SOL</tt>, specifying
1231 <tt>energygrp-excl = Protein Protein SOL SOL</tt>
1233 would give only the non-bonded interactions between the protein and the
1234 solvent. This is especially useful for speeding up energy calculations with
1235 <tt>mdrun -rerun</tt> and for excluding interactions within frozen groups.</dd>
1238 <A NAME="walls"><br>
1240 <h3>Walls<!--QuietIdx-->walls<!--EQuietIdx--></h3>
1242 <dt><b>nwall: 0</b></dt>
1243 <dd>When set to <b>1</b> there is a wall at <tt>z=0</tt>, when set to <b>2</b>
1244 there is also a wall at <tt>z=z-box</tt>. Walls can only be used with <b>pbc=xy</b>.
1245 When set to <b>2</b> pressure coupling and Ewald summation can be used
1246 (it is usually best to use semiisotropic pressure coupling with
1247 the <tt>x/y</tt> compressibility set to 0, as otherwise the surface area will change).
1248 Walls interact wit the rest of the system through an optional <tt>wall-atomtype</tt>.
1249 Energy groups <tt>wall0</tt> and <tt>wall1</tt> (for <b>nwall=2</b>) are
1250 added automatically to monitor the interaction of energy groups
1252 The <A HREF="#run">center of mass motion removal</A> will be turned
1253 off in the <tt>z</tt>-direction.</dd>
1254 <dt><b>wall-atomtype:</b></dt>
1255 <dd>the atom type name in the force field for each wall.
1256 By (for example) defining a special wall atom type in the topology with its
1257 own combination rules, this allows for independent tuning of the interaction
1258 of each atomtype with the walls.</dd>
1259 <dt><b>wall-type:</b></dt>
1262 <dd>LJ integrated over the volume behind the wall: 9-3 potential</dd>
1263 <dt><b>10-4</b></dt>
1264 <dd>LJ integrated over the wall surface: 10-4 potential</dd>
1265 <dt><b>12-6</b></dt>
1266 <dd>direct LJ potential with the z distance from the wall</dd>
1267 <dt><b>table</b></dt><dd>user defined potentials indexed with the z distance from the wall, the tables are read analogously to
1268 the <b><A HREF="#table">energygrp-table</A></b> option,
1269 where the first name is for a ``normal'' energy group and the second name
1270 is <tt>wall0</tt> or <tt>wall1</tt>,
1271 only the dispersion and repulsion columns are used</dd>
1273 <dt><b>wall-r-linpot: -1 (nm)</b></dt>
1274 <dd>Below this distance from the wall the potential is continued
1275 linearly and thus the force is constant. Setting this option to
1276 a postive value is especially useful for equilibration when some atoms
1278 When the value is ≤0 (<0 for <b>wall-type=table</b>),
1279 a fatal error is generated when atoms are beyond a wall.
1281 <dt><b>wall-density: [nm<sup>-3</sup>/nm<sup>-2</sup>]</b></dt>
1282 <dd>the number density of the atoms for each wall for wall types
1283 <b>9-3</b> and <b>10-4</b>
1284 <dt><b>wall-ewald-zfac: 3</b></dt>
1285 <dd>The scaling factor for the third box vector for Ewald summation only,
1287 Ewald summation can only be used with <b>nwall=2</b>, where one
1288 should use <b><A HREF="#ewald">ewald-geometry</A><tt>=3dc</tt></b>.
1289 The empty layer in the box serves to decrease the unphysical Coulomb
1290 interaction between periodic images.</dd>
1295 <h3>COM <!--Idx-->pulling<!--EIdx--></h3>
1297 <dt><b>pull:</b></dt>
1300 <dd>No center of mass pulling.
1301 All the following pull options will be ignored
1302 (and if present in the <tt>.mdp</tt> file, they unfortunately generate warnings)</dd>
1303 <dt><b>umbrella</b></dt>
1304 <dd>Center of mass pulling using an umbrella potential
1305 between the reference group and one or more groups.</dd>
1306 <dt><b>constraint</b></dt>
1307 <dd>Center of mass pulling using a constraint
1308 between the reference group and one or more groups.
1309 The setup is identical to the option <b>umbrella</b>, except for the fact
1310 that a rigid constraint is applied instead of a harmonic potential.</dd>
1311 <dt><b>constant-force</b></dt>
1312 <dd>Center of mass pulling using a linear potential and therefore
1313 a constant force. For this option there is no reference position
1314 and therefore the parameters <b>pull-init</b> and <b>pull-rate</b>
1317 <dt><b>pull-geometry:</b></dt>
1319 <dt><b>distance</b></dt>
1320 <dd>Pull along the vector connecting the two groups.
1321 Components can be selected with <b>pull-dim</b>.</dd>
1322 <dt><b>direction</b></dt>
1323 <dd>Pull in the direction of <b>pull-vec</b>.</dd>
1324 <dt><b>direction-periodic</b></dt>
1325 <dd>As <b>direction</b>, but allows the distance to be larger than
1326 half the box size. With this geometry the box should not be dynamic
1327 (e.g. no pressure scaling) in the pull dimensions and the pull force
1328 is not added to virial.</dd>
1329 <dt><b>cylinder</b></dt>
1330 <dd>Designed for pulling with respect to a layer where the reference COM
1331 is given by a local cylindrical part of the reference group.
1332 The pulling is in the direction of <b>pull-vec</b>.
1333 From the reference group a cylinder is selected around the axis going
1334 through the pull group with direction <b>pull-vec</b> using two radii.
1335 The radius <b>pull-r1</b> gives the radius within which all
1336 the relative weights are one, between <b>pull-r1</b> and
1337 <b>pull-r0</b> the weights are switched to zero. Mass weighting is also used.
1338 Note that the radii should be smaller than half the box size.
1339 For tilted cylinders they should be even smaller than half the box size
1340 since the distance of an atom in the reference group
1341 from the COM of the pull group has both a radial and an axial component.</dd>
1343 <dt><b>pull-dim: (Y Y Y)</b></dt>
1344 <dd>the distance components to be used with geometry <b>distance</b>
1345 and <b>position</b>, and also sets which components are printed
1346 to the output files</dd>
1347 <dt><b>pull-r1: (1) [nm]</b></dt>
1348 <dd>the inner radius of the cylinder for geometry <b>cylinder</b></dd>
1349 <dt><b>pull-r0: (1) [nm]</b></dt>
1350 <dd>the outer radius of the cylinder for geometry <b>cylinder</b></dd>
1351 <dt><b>pull-constr-tol: (1e-6)</b></dt>
1352 <dd>the relative constraint tolerance for constraint pulling</dd>
1353 <dt><b>pull-start:</b></dt>
1356 <dd>do not modify <b>pull-init</b>
1358 <dd>add the COM distance of the starting conformation to <b>pull-init</b></dd>
1360 <dt><b>pull-print-reference: (10)</b></dt>
1363 <dd>do not print the COM of the first group in each pull coordinate</dd>
1365 <dd>print the COM of the first group in each pull coordinate</dd>
1367 <dt><b>pull-nstxout: (10)</b></dt>
1368 <dd>frequency for writing out the COMs of all the pull group</dd>
1369 <dt><b>pull-nstfout: (1)</b></dt>
1370 <dd>frequency for writing out the force of all the pulled group</dd>
1371 <dt><b>pull-ngroups: (1)</b></dt>
1372 <dd>The number of pull groups, not including the absolute reference group,
1373 when used. Pull groups can be reused in multiple pull coordinates.
1374 Below only the pull options for group 1 are given, further groups simply
1375 increase the group index number.</dd>
1376 <dt><b>pull-ncoords: (1)</b></dt>
1377 <dd>The number of pull coordinates. Below only the pull options for
1378 coordinate 1 are given, further coordinates simply increase the coordinate
1381 <dt><b>pull-group1-name: </b></dt>
1382 <dd>The name of the pull group, is looked up in the index file
1383 or in the default groups to obtain the atoms involved.</dd>
1384 <dt><b>pull-group1-weights: </b></dt>
1385 <dd>Optional relative weights which are multiplied with the masses of the atoms
1386 to give the total weight for the COM. The number should be 0, meaning all 1,
1387 or the number of atoms in the pull group.</dd>
1388 <dt><b>pull-group1-pbcatom: (0)</b></dt>
1389 <dd>The reference atom for the treatment of periodic boundary conditions
1391 (this has no effect on the treatment of the pbc between groups).
1392 This option is only important when the diameter of the pull group
1393 is larger than half the shortest box vector.
1394 For determining the COM, all atoms in the group are put at their periodic image
1395 which is closest to <b>pull-group1-pbcatom</b>.
1396 A value of 0 means that the middle atom (number wise) is used.
1397 This parameter is not used with geometry <b>cylinder</b>.
1398 A value of -1 turns on cosine weighting, which is useful for a group
1399 of molecules in a periodic system, e.g. a water slab (see Engin et al.
1400 J. Chem. Phys. B 2010).</dd>
1402 <dt><b>pull-coord1-groups: </b></dt>
1403 <dd>The two groups indices should be given on which this pull coordinate
1404 will operate. The first index can be 0, in which case an absolute reference
1405 of <b>pull-coord1-origin</b> is used. With an absolute reference the system
1406 is no longer translation invariant and one should think about what to do with
1407 the <A HREF="#run">center of mass motion</A>.</dd>
1408 <dt><b>pull-coord1-origin: (0.0 0.0 0.0)</b></dt>
1409 <dd>The pull reference position for use with an absolute reference.</dd>
1410 <dt><b>pull-coord1-vec: (0.0 0.0 0.0)</b></dt>
1411 <dd>The pull direction. <tt>grompp</tt> normalizes the vector.</dd>
1412 <dt><b>pull-coord1-init: (0.0) [nm]</b></dt>
1413 <dd>The reference distance at t=0.</dd>
1414 <dt><b>pull-coord1-rate: (0) [nm/ps]</b></dt>
1415 <dd>The rate of change of the reference position.</dd>
1416 <dt><b>pull-coord1-k: (0) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
1417 <dd>The force constant. For umbrella pulling this is the harmonic force
1418 constant in [kJ mol<sup>-1</sup> nm<sup>-2</sup>]. For constant force pulling
1419 this is the force constant of the linear potential, and thus minus (!)
1420 the constant force in [kJ mol<sup>-1</sup> nm<sup>-1</sup>].</dd>
1421 <dt><b>pull-coord1-kB: (pull-k1) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
1422 <dd>As <b>pull-coord1-k</b>, but for state B. This is only used when
1423 <A HREF="#free"><b>free-energy</b></A> is turned on.
1424 The force constant is then (1 - lambda)*<b>pull-coord1-k</b> + lambda*<b>pull-coord1-kB</b></dt>.
1430 <h3><!--Idx-->NMR refinement<!--EIdx--></h3>
1432 <dt><b>disre:</b></dt>
1435 <dd>ignore <!--Idx-->distance restraint<!--EIdx--> information in topology file</dd>
1436 <dt><b>simple</b></dt>
1437 <dd>simple (per-molecule) distance restraints.
1438 <dt><b>ensemble</b></dt>
1439 <dd>distance restraints over an ensemble of molecules in one
1440 simulation box. Normally, one would perform ensemble averaging over
1441 multiple subsystems, each in a separate box, using <tt>mdrun -multi</tt>;s
1442 upply <tt>topol0.tpr</tt>, <tt>topol1.tpr</tt>, ... with different
1443 coordinates and/or velocities.
1444 The environment variable <tt>GMX_DISRE_ENSEMBLE_SIZE</tt> sets the number
1445 of systems within each ensemble (usually equal to the <tt>mdrun -multi</tt> value).</dd>
1448 <dt><b>disre-weighting:</b></dt>
1450 <dt><b>equal</b> (default)</dt>
1451 <dd>divide the restraint force equally over all atom pairs in the restraint</dd>
1452 <dt><b>conservative</b></dt>
1453 <dd>the forces are the derivative of the restraint potential,
1454 this results in an r<sup>-7</sup> weighting of the atom pairs.
1455 The forces are conservative when <tt>disre-tau</tt> is zero.</dd>
1457 <dt><b>disre-mixed:</b></dt>
1460 <dd>the violation used in the calculation of the restraint force is the
1461 time-averaged violation </dd>
1463 <dd>the violation used in the calculation of the restraint force is the
1464 square root of the product of the time-averaged violation and the instantaneous violation</dd>
1467 <dt><b>disre-fc: (1000) [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
1468 <dd>force constant for distance restraints, which is multiplied by a
1469 (possibly) different factor for each restraint given in the <tt>fac</tt>
1470 column of the interaction in the topology file.</dd>
1472 <dt><b>disre-tau: (0) [ps]</b></dt>
1473 <dd>time constant for distance restraints running average. A value of zero turns off time averaging.</dd>
1475 <dt><b>nstdisreout: (100) [steps]</b></dt>
1476 <dd>period between steps when the running time-averaged and instantaneous distances
1477 of all atom pairs involved in restraints are written to the energy file
1478 (can make the energy file very large)</dd>
1481 <dt><b>orire:</b></dt>
1484 <dd>ignore <!--Idx-->orientation restraint<!--EIdx--> information in topology file</dd>
1486 <dd>use orientation restraints, ensemble averaging can be performed
1487 with <tt>mdrun -multi</tt></dd>
1489 <dt><b>orire-fc: (0) [kJ mol]</b></dt>
1490 <dd>force constant for orientation restraints, which is multiplied by a
1491 (possibly) different weight factor for each restraint, can be set to zero to
1492 obtain the orientations from a free simulation</dd>
1493 <dt><b>orire-tau: (0) [ps]</b></dt>
1494 <dd>time constant for orientation restraints running average. A value of zero turns off time averaging.</dd>
1495 <dt><b>orire-fitgrp: </b></dt>
1496 <dd>fit group for orientation restraining. This group of atoms is used
1497 to determine the rotation <b>R</b> of the system with respect to the
1498 reference orientation. The reference orientation is the starting
1499 conformation of the first subsystem. For a protein, backbone is a reasonable
1501 <dt><b>nstorireout: (100) [steps]</b></dt>
1502 <dd>period between steps when the running time-averaged and instantaneous orientations
1503 for all restraints, and the molecular order tensor are written to the energy file
1504 (can make the energy file very large)</dd>
1509 <h3>Free energy calculations<!--QuietIdx-->free energy calculations<!--EQuietIdx--></h3>
1512 <dt><b>free-energy:</b></dt>
1515 <dd>Only use topology A.</dd>
1517 <dd>Interpolate between topology A (lambda=0) to topology B (lambda=1)
1518 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
1519 the energy file and/or to <tt>dhdl.xvg</tt>, where they can be processed by, for example <tt>g_bar</tt>.
1520 The potentials, bond-lengths and angles are interpolated linearly as
1521 described in the manual. When <b>sc-alpha</b> is larger than zero, soft-core
1522 potentials are used for the LJ and Coulomb interactions.</dd>
1523 <dt><b>expanded</b></dt>
1524 <dd> Turns on expanded ensemble simulation, where the alchemical state becomes a dynamic variable, allowing jumping between different Hamiltonians. See the <A HREF="#expanded">expanded ensemble options</A> for controlling how expanded ensemble simulations are performed. The different Hamiltonians used in expanded ensemble simulations are defined by the other free energy options.</dd>
1526 <dt><b>init-lambda: (-1)</b></dt>
1527 <dd>starting value for lambda (float). Generally, this should only be used with slow growth (i.e. nonzero <b>delta-lambda</b>). In other cases, <b>init-lambda-state</b> should be specified instead. Must be greater than or equal to 0.</dd>
1528 <dt><b>delta-lambda: (0)</b></dt>
1529 <dd>increment per time step for lambda</dd>
1530 <dt><b>init-lambda-state: (-1)</b></dt>
1531 <dd>starting value for the lambda state (integer). Specifies which columm of the lambda vector (<b>coul-lambdas</b>, <b>vdw-lambdas</b>, <b>bonded-lambdas</b>, <b>restraint-lambdas</b>, <b>mass-lambdas</b>, <b>temperature-lambdas</b>, <b>fep-lambdas</b>) should be used. This is a zero-based index: <b>init-lambda-state</b> 0 means the first column, and so on.</dd>
1532 <dt><b>fep-lambdas: ()</b></dt>
1533 <dd>Zero, one or more lambda values for which Delta H values will
1534 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps.
1535 Values must be between 0 and 1.
1536 Free energy differences between different lambda values can then
1537 be determined with <tt>g_bar</tt>. <b>fep-lambdas</b> is different from the other -lambdas keywords because
1538 all components of the lambda vector that are not specified will use <b>fep-lambdas</b> (including restraint-lambdas and therefore the pull code restraints).</dd>
1539 <dt><b>coul-lambdas: ()</b></dt>
1540 <dd>Zero, one or more lambda values for which Delta H values will
1541 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1542 Only the electrostatic interactions are controlled with this component of the lambda vector (and only if the lambda=0 and lambda=1 states have differing electrostatic interactions).</dd>
1543 <dt><b>vdw-lambdas: ()</b></dt>
1544 <dd>Zero, one or more lambda values for which Delta H values will
1545 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1546 Only the van der Waals interactions are controlled with this component of the lambda vector.</dd>
1547 <dt><b>bonded-lambdas: ()</b></dt>
1548 <dd>Zero, one or more lambda values for which Delta H values will
1549 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1550 Only the bonded interactions are controlled with this component of the lambda vector.</dd>
1551 <dt><b>restraint-lambdas: ()</b></dt>
1552 <dd>Zero, one or more lambda values for which Delta H values will
1553 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1554 Only the restraint interactions: dihedral restraints, and the pull code restraints are controlled with this component of the lambda vector. </dd>
1555 <dt><b>mass-lambdas: ()</b></dt>
1556 <dd>Zero, one or more lambda values for which Delta H values will
1557 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1558 Only the particle masses are controlled with this component of the lambda vector.</dd>
1559 <dt><b>temperature-lambdas: ()</b></dt>
1560 <dd>Zero, one or more lambda values for which Delta H values will
1561 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1562 Only the temperatures controlled with this component of the lambda vector.
1563 Note that these lambdas should not be used for replica exchange, only for simulated tempering.</dd>
1564 <dt><b>calc-lambda-neighbors (1)</b></dt>
1565 <dd>Controls the number of lambda values for which Delta H values will be
1566 calculated and written out, if <b>init-lambda-state</b> has been set. A
1567 positive value will limit the number of lambda points calculated to only the
1568 nth neighbors of <b>init-lambda-state</b>: for example, if
1569 <b>init-lambda-state</b> is 5 and this parameter has a value of 2, energies for
1570 lambda points 3-7 will be calculated and writen out. A value of -1 means all
1571 lambda points will be written out. For normal BAR such as with g_bar, a value
1572 of 1 is sufficient, while for MBAR -1 should be used.</dd>
1573 <dt><b>sc-alpha: (0)</b></dt>
1574 <dd>the soft-core alpha parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions</dd>
1575 <dt><b>sc-r-power: (6)</b></dt>
1576 <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>
1577 <dt><b>sc-coul: (no)</b></dt>
1578 <dd>Whether to apply the soft core free energy interaction transformation to the Columbic interaction of a molecule. Default is no, as it is generally
1579 more efficient to turn off the Coulomic interactions linearly before turning off the van der Waals interactions.</dd>
1580 <dt><b>sc-power: (0)</b></dt>
1581 <dd>the power for lambda in the soft-core function, only the values 1 and 2 are supported</dd>
1582 <dt><b>sc-sigma: (0.3) [nm]</b></dt>
1583 <dd>the soft-core sigma for particles which have a C6 or C12 parameter equal
1584 to zero or a sigma smaller than <b>sc-sigma</b></dd>
1585 <dt><b>couple-moltype:</b></dt>
1586 <dd>Here one can supply a molecule type (as defined in the topology)
1587 for calculating solvation or coupling free energies.
1588 There is a special option <b>system</b> that couples all molecule types
1589 in the system. This can be useful for equilibrating a system
1590 starting from (nearly) random coordinates.
1591 <b>free-energy</b> has to be turned on.
1592 The Van der Waals interactions and/or charges in this molecule type can be
1593 turned on or off between lambda=0 and lambda=1, depending on the settings
1594 of <b>couple-lambda0</b> and <b>couple-lambda1</b>. If you want to decouple
1595 one of several copies of a molecule, you need to copy and rename
1596 the molecule definition in the topology.</dd>
1597 <dt><b>couple-lambda0:</b></dt>
1599 <dt><b>vdw-q</b></dt>
1600 <dd>all interactions are on at lambda=0
1602 <dd>the charges are zero (no Coulomb interactions) at lambda=0
1604 <dd>the Van der Waals interactions are turned at lambda=0; soft-core interactions will be required to avoid singularities
1605 <dt><b>none</b></dt>
1606 <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.
1608 <dt><b>couple-lambda1:</b></dt>
1609 <dd> analogous to <b>couple-lambda1</b>, but for lambda=1
1610 <dt><b>couple-intramol:</b></dt>
1613 <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.
1615 <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.
1617 <dt><b>nstdhdl: (100)</b></dt>
1618 <dd>the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg,
1619 0 means no ouput, should be a multiple of <b>nstcalcenergy</b></dd>.</dd>
1620 <dt><b>dhdl-derivatives: (yes)</b></dt>
1621 <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>
1622 <dt><b>dhdl-print-energy: (no)</b></dt>
1623 <dd> Include the total energy in the dhdl file. This information is needed for later analysis if the states of interest in the free e energy calculation are at different temperatures. If all are at the same temperature, this information is not needed.</dd>
1624 <dt><b>separate-dhdl-file: (yes)</b></dt>
1627 <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>
1629 <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>
1631 <dt><b>dh-hist-size: (0)</b></dt>
1632 <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>
1633 <dt><b>dh-hist-spacing (0.1)</b></dt>
1634 <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>
1636 <A NAME="expanded"><br>
1638 <h3><!--Idx-->Expanded Ensemble calculations<!--EIdx--></h3>
1641 <dt><b>nstexpanded</b></dt> <dd>The number of integration steps beween attempted moves changing the system Hamiltonian in expanded ensemble simulations. Must be a multiple of <b>nstcalcenergy</b>, but can be greater or less than <b>nstdhdl</b>.</dd>
1642 <dt><b>lmc-stats:</b></dt>
1645 <dd>No Monte Carlo in state space is performed.</dd>
1646 <dt><b>metropolis-transition</b></dt>
1647 <dd> Uses the Metropolis weights to update the expanded ensemble weight of each state.
1648 Min{1,exp(-(beta_new u_new - beta_old u_old)}</dd>
1649 <dt><b>barker-transition</b></dt>
1650 <dd> Uses the Barker transition critera to update the expanded ensemble weight of each state i, defined by
1651 exp(-beta_new u_new)/[exp(-beta_new u_new)+exp(-beta_old u_old)</dd>
1652 <dt><b>wang-landau</b></dt>
1653 <dd>Uses the Wang-Landau algorithm (in state space, not energy space) to update the expanded ensemble weights.</dd>
1654 <dt><b>min-variance</b></dt>
1655 <dd>Uses the minimum variance updating method of Escobedo et al. to update the expanded ensemble weights. Weights
1656 will not be the free energies, but will rather emphasize states that need more sampling to give even uncertainty.</dd>
1658 <dt><b>lmc-mc-move:</b></dt>
1661 <dd>No Monte Carlo in state space is performed.</dd>
1662 <dt><b>metropolis-transition</b></dt>
1663 <dd> Randomly chooses a new state up or down, then uses the Metropolis critera to decide whether to accept or reject:
1664 Min{1,exp(-(beta_new u_new - beta_old u_old)}</dd>
1665 <dt><b>barker-transition</b></dt>
1666 <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>
1667 <dt><b>gibbs</b></dt>
1668 <dd> Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to
1669 decide which state to move to.</dd>
1670 <dt><b>metropolized-gibbs</b></dt>
1672 <dd> Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to
1673 decide which state to move to, EXCLUDING the current state, then uses a rejection step to ensure detailed
1674 balance. Always more efficient that Gibbs, though only marginally so in many situations, such as when only the nearest neighbors have decent phase space overlap.</dd>
1676 <dt><b>lmc-seed:</b></dt>
1677 <dd> random seed to use for Monte Carlo moves in state space. If not specified, <b>ld-seed</b> is used instead.</dd>
1678 <dt><b>mc-temperature:</b></dt>
1679 <dd> Temperature used for acceptance/rejection for Monte Carlo moves. If not specified, the temperature of the
1680 simulation specified in the first group of <b>ref_t</b> is used.</dd>
1681 <dt><b>wl-ratio: (0.8)</b></dt>
1682 <dd>The cutoff for the histogram of state occupancies to be reset, and the free energy incrementor to be reset as delta -> delta*wl-scale. If we define the Nratio = (number of samples at each histogram) / (average number of samples at each histogram). <b>wl-ratio</b> of 0.8 means that means that the histogram is only considered flat if all Nratio > 0.8 AND simultaneously all 1/Nratio > 0.8.</dd>
1683 <dt><b>wl-scale: (0.8)</b></dt>
1684 <dd> Each time the histogram is considered flat, then the current value of the Wang-Landau incrementor for the free energies is multiplied by <b>wl-scale</b>. Value must be between 0 and 1.</dd>
1685 <dt><b>init-wl-delta: (1.0)</b></dt>
1686 <dd>The initial value of the Wang-Landau incrementor in kT. Some value near 1 kT is usually most efficient, though sometimes a value of 2-3 in units of kT works better if the free energy differences are large.</dd>
1687 <dt><b>wl-oneovert: (no)</b></dt>
1688 <dd>Set Wang-Landau incrementor to scale with 1/(simulation time) in the large sample limit. There is significant evidence that the standard Wang-Landau algorithms in state space presented here result in free energies getting 'burned in' to incorrect values that depend on the initial state. when <b>wl-oneovert</b> is true, then when the incrementor becomes less than 1/N, where N is the mumber of samples collected (and thus proportional to the data collection time, hence '1 over t'), then the Wang-Lambda incrementor is set to 1/N, decreasing every step. Once this occurs, <b>wl-ratio</b> is ignored, but the weights will still stop updating when the equilibration criteria set in <b>lmc-weights-equil</b> is achieved.</dd>
1689 <dt><b>lmc-repeats: (1)</b></dt>
1690 <dd>Controls the number of times that each Monte Carlo swap type is performed each iteration. In the limit of large numbers of Monte Carlo repeats, then all methods converge to Gibbs sampling. The value will generally not need to be different from 1.</dd>
1691 <dt><b>lmc-gibbsdelta: (-1)</b></dt>
1692 <dd> Limit Gibbs sampling to selected numbers of neighboring states. For Gibbs sampling, it is sometimes inefficient to perform Gibbs sampling over all of the states that are defined. A positive value of <b>lmc-gibbsdelta</b> means that only states plus or minus <b>lmc-gibbsdelta</b> are considered in exchanges up and down. A value of -1 means that all states are considered. For less than 100 states, it is probably not that expensive to include all states.</dd>
1693 <dt><b>lmc-forced-nstart: (0)</b></dt>
1694 <dd> Force initial state space sampling to generate weights. In order to come up with reasonable initial weights, this setting allows the simulation to drive from the initial to the final lambda state, with <b>lmc-forced-nstart</b> steps at each state before moving on to the next lambda state. If <b>lmc-forced-nstart</b> is sufficiently long (thousands of steps, perhaps), then the weights will be close to correct. However, in most cases, it is probably better to simply run the standard weight equilibration algorithms.
1695 <dt><b>nst-transition-matrix: (-1)</b></dt>
1696 <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>
1697 <dt><b>symmetrized-transition-matrix: (no) </b></dt>
1698 <dd>Whether to symmetrize the empirical transition matrix. In the infinite limit the matrix will be symmetric, but will diverge with statistical noise for short timescales. Forced symmetrization, by using the matrix T_sym = 1/2 (T + transpose(T)), removes problems like the existence of (small magnitude) negative eigenvalues.</dd>
1699 <dt><b>mininum-var-min: (100)</b></dt>
1700 <dd> The <b>min-variance</b> strategy (option of <b>lmc-stats</b> is only valid for larger number of samples, and can get stuck if too few samples are used at each state. <b>mininum-var-min</b> is the minimum number of samples that each state that are allowed before the <b>min-variance</b> strategy is activated if selected.</dd>
1701 <dt><b>init-lambda-weights: </b></dt>
1702 <dd>The initial weights (free energies) used for the expanded ensemble states. Default is a vector of zero weights. format is similar to the lambda vector settings in <b>fep-lambdas</b>, except the weights can be any floating point number. Units are kT. Its length must match the lambda vector lengths.</dd>
1703 <dt><b>lmc-weights-equil: (no)</b></dt>
1706 <dd>Expanded ensemble weights continue to be updated throughout the simulation.</dd>
1708 <dd>The input expanded ensemble weights are treated as equilibrated, and are not updated throughout the simulation.</dd>
1709 <dt><b>wl-delta</b></dt>
1710 <dd>Expanded ensemble weight updating is stopped when the Wang-Landau incrementor falls below the value specified by <b>weight-equil-wl-delta</b>.</dd>
1711 <dt><b>number-all-lambda</b></dt>
1712 <dd>Expanded ensemble weight updating is stopped when the number of samples at all of the lambda states is greater than the value specified by <b>weight-equil-number-all-lambda</b>.</dd>
1713 <dt><b>number-steps</b></dt>
1714 <dd>Expanded ensemble weight updating is stopped when the number of steps is greater than the level specified by <b>weight-equil-number-steps</b>.</dd>
1715 <dt><b>number-samples</b></dt>
1716 <dd>Expanded ensemble weight updating is stopped when the number of total samples across all lambda states is greater than the level specified by <b>weight-equil-number-samples</b>.</dd>
1717 <dt><b>count-ratio</b></dt>
1718 <dd>Expanded ensemble weight updating is stopped when the ratio of samples at the least sampled lambda state and most sampled lambda state greater than the value specified by <b>weight-equil-count-ratio</b>.</dd>
1720 <dt><b>simulated-tempering: (no)</b></dt>
1721 <dd>Turn simulated tempering on or off. Simulated tempering is implemented as expanded ensemble sampling with different temperatures instead of different Hamiltonians.</dd>
1722 <dt><b>sim-temp-low: (300)</b></dt>
1723 <dd>Low temperature for simulated tempering.</dd>
1724 <dt><b>sim-temp-high: (300)</b></dt>
1725 <dd>High temperature for simulated tempering.</dd>
1726 <dt><b>simulated-tempering-scaling: (linear)</b></dt>
1727 <dd>Controls the way that the temperatures at intermediate lambdas are calculated from the <b>temperature-lambda</b> part of the lambda vector.</dd>
1729 <dt><b>linear</b></dt>
1730 <dd>Linearly interpolates the temperatures using the values of <b>temperature-lambda</b>,i.e. if <b>sim-temp-low</b>=300, <b>sim-temp-high</b>=400, then lambda=0.5 correspond to a temperature of 350. A nonlinear set of temperatures can always be implemented with uneven spacing in lambda.</dd>
1731 <dt><b>geometric</b></dt>
1732 <dd> Interpolates temperatures geometrically between <b>sim-temp-low</b> and <b>sim-temp-high</b>. The i:th state has temperature <b>sim-temp-low</b> * (<b>sim-temp-high</b>/<b>sim-temp-low</b>) raised to the power of (i/(ntemps-1)). This should give roughly equal exchange for constant heat capacity, though of course things simulations that involve protein folding have very high heat capacity peaks.</dd>
1733 <dt><b>exponential</b></dt>
1734 <dd> Interpolates temperatures exponentially between <b>sim-temp-low</b> and <b>sim-temp-high</b>. The ith state has temperature
1735 <b>sim-temp-low</b> + (<b>sim-temp-high</b>-<b>sim-temp-low</b>)*((exp(<b>temperature-lambdas</b>[i])-1)/(exp(1.0)-1)).</dd>
1741 <h3>Non-equilibrium MD<!--QuietIdx-->non-equilibrium MD<!--EQuietIdx--></h3>
1744 <dt><b>acc-grps: </b></dt>
1745 <dd>groups for constant acceleration (e.g.: <tt>Protein Sol</tt>)
1746 all atoms in groups Protein and Sol will experience constant acceleration
1747 as specified in the <b>accelerate</b> line</dd>
1748 <dt><b>accelerate: (0) [nm ps<sup>-2</sup>]</b></dt>
1749 <dd>acceleration for <b>acc-grps</b>; x, y and z for each group
1750 (e.g. <tt>0.1 0.0 0.0 -0.1 0.0 0.0</tt> means that first group has constant
1751 acceleration of 0.1 nm ps<sup>-2</sup> in X direction, second group the
1753 <dt><b>freezegrps: </b></dt>
1754 <dd>Groups that are to be frozen (i.e. their X, Y, and/or Z position will
1755 not be updated; e.g. <tt>Lipid SOL</tt>). <b>freezedim</b> specifies for
1756 which dimension the freezing applies.
1757 To avoid spurious contibrutions to the virial and pressure due to large
1758 forces between completely frozen atoms you need to use
1759 <A HREF="#egexcl">energy group exclusions</A>, this also saves computing time.
1760 Note that coordinates of frozen atoms are not scaled by pressure-coupling
1762 <dt><b>freezedim: </b></dt>
1763 <dd>dimensions for which groups in <b>freezegrps</b> should be frozen,
1764 specify <tt>Y</tt> or <tt>N</tt> for X, Y and Z and for each group
1765 (e.g. <tt>Y Y N N N N</tt> means that particles in the first group
1766 can move only in Z direction. The particles in the second group can
1767 move in any direction).</dd>
1768 <dt><b>cos-acceleration: (0) [nm ps<sup>-2</sup>]</b></dt>
1769 <dd>the amplitude of the acceleration profile for calculating the
1770 <!--Idx-->viscosity<!--EIdx-->.
1771 The acceleration is in the X-direction and the magnitude is
1772 <b>cos-acceleration</b> cos(2 pi z/boxheight).
1773 Two terms are added to the energy file:
1774 the amplitude of the velocity profile and 1/viscosity.</dd>
1775 <dt><b><!--Idx-->deform<!--EIdx-->: (0 0 0 0 0 0) [nm ps<sup>-1</sup>]</b></dt>
1776 <dd>The velocities of deformation for the box elements:
1777 a(x) b(y) c(z) b(x) c(x) c(y). Each step the box elements
1778 for which <b>deform</b> is non-zero are calculated as:
1779 box(ts)+(t-ts)*deform, off-diagonal elements are corrected
1780 for periodicity. The coordinates are transformed accordingly.
1781 Frozen degrees of freedom are (purposely) also transformed.
1782 The time ts is set to t at the first step and at steps at which
1783 x and v are written to trajectory to ensure exact restarts.
1784 Deformation can be used together with semiisotropic or anisotropic
1785 pressure coupling when the appropriate compressibilities are set to zero.
1786 The diagonal elements can be used to <!--Idx-->strain<!--EIdx--> a solid.
1787 The off-diagonal elements can be used to <!--Idx-->shear<!--EIdx--> a solid
1793 <h3>Electric fields<!--QuietIdx-->electric field<!--EQuietIdx--></h3>
1796 <dt><b>E-x ; E-y ; E-z:</b></dt>
1797 <dd>If you want to use an electric field in a direction, enter 3 numbers
1798 after the appropriate <b>E-*</b>, the first number: the number of cosines,
1799 only 1 is implemented (with frequency 0) so enter 1,
1800 the second number: the strength of the electric field in
1801 <b>V nm<sup>-1</sup></b>,
1802 the third number: the phase of the cosine, you can enter any number here
1803 since a cosine of frequency zero has no phase.</dd>
1804 <dt><b>E-xt; E-yt; E-zt: </b></dt>
1805 <dd>not implemented yet</dd>
1811 <h3>Mixed quantum/classical molecular dynamics<!--QuietIdx>QM/MM<!--EQuietIdx--></h3>
1814 <dt><b>QMMM:</b></dt>
1815 <dd><dl compact="compact">
1819 <dd>Do a QM/MM simulation. Several groups can be described at
1820 different QM levels separately. These are specified in
1821 the <b>QMMM-grps</b> field separated by spaces. The level of <i>ab
1822 initio</i> theory at which the groups are described is specified
1823 by <b>QMmethod</b> and <b>QMbasis</b> Fields. Describing the
1824 groups at different levels of theory is only possible with the ONIOM
1825 QM/MM scheme, specified by <b>QMMMscheme</b>.</dd>
1828 <dt><b>QMMM-grps:</b></dt>
1829 <dd>groups to be descibed at the QM level</dd>
1831 <dt><b>QMMMscheme:</b></dt>
1832 <dd><dl compact="compact">
1833 <dt><b>normal</b></dt>
1834 <dd>normal QM/MM. There can only be one <b>QMMM-grps</b> that is modelled
1835 at the <b>QMmethod</b> and <b>QMbasis</b> level of <i>ab initio</i>
1836 theory. The rest of the system is described at the MM level. The QM
1837 and MM subsystems interact as follows: MM point charges are included
1838 in the QM one-electron hamiltonian and all Lennard-Jones interactions
1839 are described at the MM level.</dd>
1840 <dt><b>ONIOM</b></dt>
1841 <dd>The interaction between the subsystem is described using the ONIOM
1842 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
1843 (<b>QMmethod</b> and <b>QMbasis</b>).
1846 <dt><b>QMmethod: (RHF)</b></dt>
1847 <dd>Method used to compute the energy and gradients on the QM
1848 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
1849 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
1850 included in the active space is specified by <b>CASelectrons</b>
1851 and <b>CASorbitals</b>. </dd>
1853 <dt><b>QMbasis: (STO-3G)</b></dt>
1854 <dd>Basis set used to expand the electronic wavefuntion. Only Gaussian
1855 basis sets are currently available, <i>i.e.</i> STO-3G, 3-21G, 3-21G*,
1856 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*, and 6-311G.</dd>
1858 <dt><b>QMcharge: (0) [integer]</b></dt>
1859 <dd>The total charge in <tt>e</tt> of the <b>QMMM-grps</b>. In case
1860 there are more than one <b>QMMM-grps</b>, the total charge of each
1861 ONIOM layer needs to be specified separately.</dd>
1863 <dt><b>QMmult: (1) [integer]</b></dt>
1864 <dd>The multiplicity of the <b>QMMM-grps</b>. In case there are more
1865 than one <b>QMMM-grps</b>, the multiplicity of each ONIOM layer needs
1866 to be specified separately.</dd>
1868 <dt><b>CASorbitals: (0) [integer]</b></dt>
1869 <dd>The number of orbitals to be included in the active space when
1870 doing a CASSCF computation.</dd>
1872 <dt><b>CASelectrons: (0) [integer]</b></dt>
1873 <dd>The number of electrons to be included in the active space when
1874 doing a CASSCF computation.</dd>
1877 <dd><dl compact="compact">
1879 <dd>No surface hopping. The system is always in the electronic
1882 <dd>Do a QM/MM MD simulation on the excited state-potential energy
1883 surface and enforce a <i>diabatic</i> hop to the ground-state when the
1884 system hits the conical intersection hyperline in the course the
1885 simulation. This option only works in combination with the CASSCF
1892 <h3>Implicit solvent</h3>
1895 <dt><b>implicit-solvent:</b></dt>
1896 <dd><dl compact="compact">
1898 <dd>No implicit solvent</dd>
1899 <dt><b>GBSA</b></dt>
1900 <dd>Do a simulation with implicit solvent using the Generalized Born formalism.
1901 Three different methods for calculating the Born radii are available, Still, HCT and
1902 OBC. These are specified with the <b>gb-algorithm</b> field. The non-polar solvation
1903 is specified with the <b>sa-algorithm</b> field.</dd>
1906 <dt><b>gb-algorithm:</b></dt>
1907 <dd><dl compact="compact">
1908 <dt><b>Still</b></dt>
1909 <dd>Use the Still method to calculate the Born radii</dd>
1911 <dd>Use the Hawkins-Cramer-Truhlar method to calculate the Born radii</dd>
1913 <dd>Use the Onufriev-Bashford-Case method to calculate the Born radii</dd>
1916 <dt><b>nstgbradii: (1) [steps]</b></dt>
1917 <dd>Frequency to (re)-calculate the Born radii. For most practial purposes,
1918 setting a value larger than 1 violates energy conservation and leads to
1919 unstable trajectories.</dd>
1921 <dt><b>rgbradii: (1.0) [nm]</b></dt>
1922 <dd>Cut-off for the calculation of the Born radii. Currently must be equal to rlist</dd>
1924 <dt><b>gb-epsilon-solvent: (80)</b></dt>
1925 <dd>Dielectric constant for the implicit solvent</dd>
1927 <dt><b>gb-saltconc: (0) [M]</b></dt>
1928 <dd>Salt concentration for implicit solvent models, currently not used</dd>
1930 <dt><b>gb-obc-alpha (1); gb-obc-beta (0.8); gb-obc-gamma (4.85);</b></dt>
1931 <dd>Scale factors for the OBC model. Default values are OBC(II).
1932 Values for OBC(I) are 0.8, 0 and 2.91 respectively</dd>
1934 <dt><b>gb-dielectric-offset: (0.009) [nm]</b></dt>
1935 <dd>Distance for the di-electric offset when calculating the Born radii. This is
1936 the offset between the center of each atom the center of the polarization energy
1937 for the corresponding atom</dd>
1939 <dt><b>sa-algorithm</b></dt>
1940 <dd><dl compact="compact">
1941 <dt><b>Ace-approximation</b></dt>
1942 <dd>Use an Ace-type approximation (default)</dd>
1943 <dt><b>None</b></dt>
1944 <dd>No non-polar solvation calculation done. For GBSA only the polar part gets
1948 <dt><b>sa-surface-tension: [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
1949 <dd>Default value for surface tension with SA algorithms. The default value is -1;
1950 Note that if this default value is not changed
1951 it will be overridden by <tt>grompp</tt> using values that are specific for the choice
1952 of radii algorithm (0.0049 kcal/mol/Angstrom<sup>2</sup> for Still, 0.0054 kcal/mol/Angstrom<sup>2</sup>
1955 Setting it to 0 will while using an sa-algorithm other than None means
1956 no non-polar calculations are done.
1960 <A NAME="adress"><br>
1962 <h3>Adaptive Resolution Simulation</h3>
1965 <dt><b>adress: (no)</b></dt>
1966 <dd>Decide whether the AdResS feature is turned on.</dd>
1967 <dt><b>adress-type: (Off)</b></dt>
1970 <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>
1971 <dt><b>Constant</b></dt>
1972 <dd>Do an AdResS simulation with a constant weight, <b>adress-const-wf</b> defines the value of the weight</dd>
1973 <dt><b>XSplit</b></dt>
1974 <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>
1975 <dt><b>Sphere</b></dt>
1976 <dd>Do an AdResS simulation with spherical explicit zone.</dd>
1978 <dt><b>adress-const-wf: (1)</b></dt>
1979 <dd>Provides the weight for a constant weight simulation (<b>adress-type</b>=Constant)</dd>
1980 <dt><b>adress-ex-width: (0)</b></dt>
1981 <dd>Width of the explicit zone, measured from <b>adress-reference-coords</b>.</dd>
1982 <dt><b>adress-hy-width: (0)</b></dt>
1983 <dd>Width of the hybrid zone.</dd>
1984 <dt><b>adress-reference-coords: (0,0,0)</b></dt>
1985 <dd>Position of the center of the explicit zone. Periodic boundary conditions apply for measuring the distance from it.</dd>
1986 <dt><b>adress-cg-grp-names</b></dt>
1987 <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>
1988 <dt><b>adress-site: (COM)</b>The mapping point from which the weight is calculated.</dt>
1991 <dd>The weight is calculated from the center of mass of each charge group.</dd>
1993 <dd>The weight is calculated from the center of geometry of each charge group.</dd>
1994 <dt><b>Atom</b></dt>
1995 <dd>The weight is calculated from the position of 1st atom of each charge group.</dd>
1996 <dt><b>AtomPerAtom</b></dt>
1997 <dd>The weight is calculated from the position of each individual atom.</dd>
1999 <dt><b>adress-interface-correction: (Off)</b></dt>
2002 <dd>Do not a apply any interface correction.</dd>
2003 <dt><b>thermoforce</b></dt>
2004 <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>
2006 <dt><b>adress-tf-grp-names</b></dt>
2007 <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>
2008 <dt><b>adress-ex-forcecap: (0)</b></dt>
2009 <dd>Cap the force in the hybrid region, useful for big molecules. 0 disables force capping.</dd>
2014 <h3>User defined thingies</h3>
2017 <dt><b>user1-grps; user2-grps: </b></dt>
2018 <dt><b>userint1 (0); userint2 (0); userint3 (0); userint4 (0)</b></dt>
2019 <dt><b>userreal1 (0); userreal2 (0); userreal3 (0); userreal4 (0)</b></dt>
2020 <dd>These you can use if you modify code. You can pass integers and
2021 reals to your subroutine. Check the inputrec definition in
2022 <tt>src/include/types/inputrec.h</tt></dd>
2033 <A HREF="#neq">acc-grps</A><br>
2034 <A HREF="#neq">accelerate</A><br>
2035 <A HREF="#sa">annealing</A><br>
2036 <A HREF="#sa">annealing-npoints</A><br>
2037 <A HREF="#sa">annealing-time</A><br>
2038 <A HREF="#sa">annealing-temp</A><br>
2039 <A HREF="#ld">bd-fric</A><br>
2040 <A HREF="#vdw">bDispCorr</A><br>
2041 <A HREF="#run">comm-mode</A><br>
2042 <A HREF="#run">comm-grps</A><br>
2043 <A HREF="#pc">compressibility</A><br>
2044 <A HREF="#bond">constraint-algorithm</A><br>
2045 <A HREF="#bond">constraints</A><br>
2046 <A HREF="#neq">cos-acceleration</A><br>
2047 <A HREF="#el">coulombtype</A><br>
2048 <A HREF="#el">coulomb-modifier</A><br>
2049 <A HREF="#free">couple-intramol</A><br>
2050 <A HREF="#free">couple-lambda0</A><br>
2051 <A HREF="#free">couple-lambda1</A><br>
2052 <A HREF="#free">couple-moltype</A><br>
2053 <A HREF="#nl">cutoff-scheme</A><br>
2054 <A HREF="#pp">define</A><br>
2055 <A HREF="#neq">deform</A><br>
2056 <A HREF="#free">delta-lambda</A><br>
2057 <A HREF="#nmr">disre</A><br>
2058 <A HREF="#nmr">disre-weighting</A><br>
2059 <A HREF="#nmr">disre-mixed</A><br>
2060 <A HREF="#nmr">disre-fc</A><br>
2061 <A HREF="#nmr">disre-tau</A><br>
2062 <A HREF="#run">dt</A><br>
2063 <A HREF="#em">emstep</A><br>
2064 <A HREF="#em">emtol</A><br>
2065 <A HREF="#egexcl">energygrp-excl</A><br>
2066 <A HREF="#table">energygrp-table</A><br>
2067 <A HREF="#out">energygrps</A><br>
2068 <A HREF="#el2">epsilon-r</A><br>
2069 <A HREF="#el2">epsilon-rf</A><br>
2070 <A HREF="#ewald">ewald-rtol</A><br>
2071 <A HREF="#ewald">ewald-geometry</A><br>
2072 <A HREF="#ewald">epsilon-surface</A><br>
2073 <A HREF="#ef">E-x</A><br>
2074 <A HREF="#ef">E-xt</A><br>
2075 <A HREF="#ef">E-y</A><br>
2076 <A HREF="#ef">E-yt</A><br>
2077 <A HREF="#ef">E-z</A><br>
2078 <A HREF="#ef">E-zt </A><br>
2079 <A HREF="#shellmd">fcstep</A><br>
2080 <A HREF="#ewald">fourier-nx</A><br>
2081 <A HREF="#ewald">fourier-ny</A><br>
2082 <A HREF="#ewald">fourier-nz</A><br>
2083 <A HREF="#ewald">fourierspacing</A><br>
2084 <A HREF="#free">free-energy</A><br>
2085 <A HREF="#neq">freezedim </A><br>
2086 <A HREF="#neq">freezegrps</A><br>
2087 <A HREF="#vel">gen-seed</A><br>
2088 <A HREF="#vel">gen-temp</A><br>
2089 <A HREF="#vel">gen-vel</A><br>
2090 <A HREF="#pp">include</A><br>
2091 <A HREF="#free">init-lambda</A><br>
2092 <A HREF="#expanded">init-lambda-weights</A><br>
2093 <A HREF="#run">init-step</A><br>
2094 <A HREF="#expanded">initial-wl-delta</A><br>
2095 <A HREF="#run">integrator</A><br>
2096 <A HREF="#ld">ld-seed</A><br>
2097 <A HREF="#bond2">lincs-iter</A><br>
2098 <A HREF="#bond2">lincs-order</A><br>
2099 <A HREF="#bond2">lincs-warnangle</A><br>
2100 <A HREF="#expanded">lmc-forced-nstart</A><br>
2101 <A HREF="#expanded">lmc-gibbsdelta</A><br>
2102 <A HREF="#expanded">lmc-mc-move</A><br>
2103 <A HREF="#expanded">lmc-seed</A><br>
2104 <A HREF="#expanded">lmc-stats</A><br>
2105 <A HREF="#expanded">lmc-weights-equil</A><br>
2106 <A HREF="#expanded">mc-temperature</A><br>
2107 <A HREF="#expanded">mininum-var-min</A><br>
2108 <A HREF="#bond2">morse</A><br>
2109 <A HREF="#em">nbfgscorr</A><br>
2110 <A HREF="#shellmd">niter</A><br>
2111 <A HREF="#tc">nh-chain-length</A><br>
2112 <A HREF="#em">nstcgsteep</A><br>
2113 <A HREF="#out">nstcalcenergy</A><br>
2114 <A HREF="#run">nstcomm</A><br>
2115 <A HREF="#nmr">nstdisreout</A><br>
2116 <A HREF="#out">nstenergy</A><br>
2117 <A HREF="#run">nsteps</A><br>
2118 <A HREF="#out">nstfout</A><br>
2119 <A HREF="#nl">nstlist</A><br>
2120 <A HREF="#out">nstlog</A><br>
2121 <A HREF="#pc">nstpcouple</A><br>
2122 <A HREF="#tc">nsttcouple</A><br>
2123 <A HREF="#out">nstvout</A><br>
2124 <A HREF="#out">nstxout</A><br>
2125 <A HREF="#out">nstxout-compressed</A><br>
2126 <A HREF="#expanded">nst-transition-matrix</A><br>
2127 <A HREF="#nl">ns-type</A><br>
2128 <A HREF="#wall">nwall</A><br>
2129 <A HREF="#ewald">optimize-fft</A><br>
2130 <A HREF="#nmr2">orire</A><br>
2131 <A HREF="#nmr2">orire-fc</A><br>
2132 <A HREF="#nmr2">orire-tau</A><br>
2133 <A HREF="#nmr2">orire-fitgrp</A><br>
2134 <A HREF="#nmr2">nstorireout</A><br>
2135 <A HREF="#nl">pbc</A><br>
2136 <A HREF="#pc">pcoupl</A><br>
2137 <A HREF="#pc">pcoupltype</A><br>
2138 <A HREF="#nl">periodic-molecules</A><br>
2139 <A HREF="#ewald">pme-order</A><br>
2140 <A HREF="#pull">pull</A><br>
2141 <A HREF="#pc">refcoord-scaling</A><br>
2142 <A HREF="#pc">ref-p</A><br>
2143 <A HREF="#tc">ref-t</A><br>
2144 <A HREF="#el2">rcoulomb-switch</A><br>
2145 <A HREF="#el2">rcoulomb</A><br>
2146 <A HREF="#nl">rlist</A><br>
2147 <A HREF="#nl">rlistlong</A><br>
2148 <A HREF="#tpi">rtpi</A><br>
2149 <A HREF="#vdw">rvdw-switch</A><br>
2150 <A HREF="#vdw">rvdw</A><br>
2151 <A HREF="#free">sc-alpha</A><br>
2152 <A HREF="#free">sc-power</A><br>
2153 <A HREF="#free">sc-sigma</A><br>
2154 <A HREF="#bond2">shake-tol</A><br>
2155 <A HREF="#expanded">sim-temp-low</A><br>
2156 <A HREF="#expanded">sim-temp-high</A><br>
2157 <A HREF="#expanded">simulated-tempering</A><br>
2158 <A HREF="#expanded">simulated-tempering-scaling</A><br>
2159 <A HREF="#expanded">symmetrized-transition-matrix</A><br>
2160 <A HREF="#table">table-extension</A><br>
2161 <A HREF="#pc">tau-p</A><br>
2162 <A HREF="#tc">tau-t</A><br>
2163 <A HREF="#tc">tc-grps</A><br>
2164 <A HREF="#tc">tcoupl</A><br>
2165 <A HREF="#run">tinit</A><br>
2166 <A HREF="#bond">continuation</A><br>
2167 <A HREF="#user">user1-grps</A><br>
2168 <A HREF="#user">user2-grps</A><br>
2169 <A HREF="#user">userint1</A><br>
2170 <A HREF="#user">userint2</A><br>
2171 <A HREF="#user">userint3</A><br>
2172 <A HREF="#user">userint4</A><br>
2173 <A HREF="#user">userreal1</A><br>
2174 <A HREF="#user">userreal2</A><br>
2175 <A HREF="#user">userreal3</A><br>
2176 <A HREF="#user">userreal4</A><br>
2177 <A HREF="#vdw">vdwtype</A><br>
2178 <A HREF="#vdw">vdw-modifier</A><br>
2179 <A HREF="#nl">verlet-buffer-tolerance</A><br>
2180 <A HREF="#out">compressed-x-grps</A><br>
2181 <A HREF="#out">compressed-x-precision</A><br>
2182 <A HREF="#sa">zero-temp-time</A><br>
2183 <A HREF="#walls">wall-atomtype</A><br>
2184 <A HREF="#walls">wall-density</A><br>
2185 <A HREF="#walls">wall-ewald-zfac</A><br>
2186 <A HREF="#walls">wall-r-linpot</A><br>
2187 <A HREF="#walls">wall-type</A><br>
2188 <A HREF="#expanded">weight-equil-count-ratio</A><br>
2189 <A HREF="#expanded">weight-equil-number-all-lambda</A><br>
2190 <A HREF="#expanded">weight-equil-number-samples</A><br>
2191 <A HREF="#expanded">weight-equil-number-steps</A><br>
2192 <A HREF="#expanded">weight-equil-wl-delta</A><br>
2193 <A HREF="#expanded">wl-ratio</A><br>
2194 <A HREF="#expanded">wl-scale</A><br>