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11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdp options</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p> </p><B>VERSION 4.6<br>
13 Sat 19 Jan 2013</B></td></tr></TABLE>
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26 <H3>Table of Contents</H3>
29 <li><A HREF="#general"><b>General remarks</b></A>
31 <li><A HREF="#pp"><b>preprocessing</b></A> (include, define)
32 <li><A HREF="#run"><b>run control</b></A> (integrator, tinit, dt, nsteps, init-step, comm-mode, nstcomm, comm-grps)
33 <li><A HREF="#ld"><b>langevin dynamics</b></A> (bd-fric, ld-seed)
34 <li><A HREF="#em"><b>energy minimization</b></A> (emtol, emstep, nstcgsteep)
35 <li><a HREF="#xmdrun"><b>shell molecular dynamics</b></a>(emtol,niter,fcstep)
36 <li><a HREF="#tpi"><b>test particle insertion</b></a>(rtpi)
37 <li><A HREF="#out"><b>output control</b></A> (nstxout, nstvout, nstfout, nstlog, nstcalcenergy, nstenergy, nstxtcout, xtc-precision, xtc-grps, energygrps)
38 <li><A HREF="#nl"><b>neighbor searching</b></A> (cutoff-scheme, nstlist, nstcalclr, ns-type, pbc, periodic-molecules, verlet-buffer-drift, rlist, rlistlong)
39 <li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, coulomb-modifier, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
40 <li><A HREF="#vdw"><b>VdW</b></A> (vdwtype, vdw-modifier, rvdw-switch, rvdw, DispCorr)
41 <li><A HREF="#table"><b>tables</b></A> (table-extension, energygrp-table)
42 <li><A HREF="#ewald"><b>Ewald</b></A> (fourierspacing, fourier-nx, fourier-ny, fourier-nz, pme-order, ewald-rtol, ewald-geometry, epsilon-surface, optimize-fft)
43 <li><A HREF="#tc"><b>Temperature coupling</b></A> (tcoupl, nsttcouple, tc-grps, tau-t, ref-t)
44 <li><A HREF="#pc"><b>Pressure coupling</b></A> (pcoupl, pcoupltype,
45 nstpcouple, tau-p, compressibility, ref-p, refcoord-scaling)
46 <li><A HREF="#sa"><b>simulated annealing</b></A> (annealing, annealing-npoints, annealing-time, annealing-temp)
47 <li><A HREF="#vel"><b>velocity generation</b></A> (gen-vel, gen-temp, gen-seed)
48 <li><A HREF="#bond"><b>bonds</b></A> (constraints, constraint-algorithm, continuation, shake-tol, lincs-order, lincs-iter, lincs-warnangle, morse)
49 <li><A HREF="#egexcl"><b>Energy group exclusions</b></A> (energygrp-excl)
50 <li><A HREF="#walls"><b>Walls</b></A> (nwall, wall-type, wall-r-linpot, wall-atomtype,
51 wall-density, wall-ewald-zfac)
52 <li><A HREF="#pull"><b>COM pulling</b></A> (pull, ...)
53 <li><A HREF="#nmr"><b>NMR refinement</b></A> (disre, disre-weighting, disre-mixed, disre-fc, disre-tau, nstdisreout, orire, orire-fc, orire-tau, orire-fitgrp, nstorireout)
54 <li><A HREF="#free"><b>Free energy calculations</b></A> (free-energy, 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)
55 <li><A HREF="#expanded"><b>Expanded ensemble simulation</b></A> (lmc-stats, lmc-mc-move, lmc-seed, lmc-gibbsdelta, mc-temperature, nst-transition-matrix, init-lambda-weights, initial-wl-delta, wl-scale, wl-ratio, symmetrized-transition-matrix, lmc-forced-nstart, mininum-var-min, lmc-weights-equil, weight-equil-wl-delta, weight-equil-number-all-lambda, weight-equil-number-steps, weight-equil-number-samples, weight-equil-count-ratio, simulated-tempering, simulated-tempering-scaling, sim-temp-low, sim-temp-high)
56 <li><A HREF="#neq"><b>Non-equilibrium MD</b></A> (acc-grps, accelerate, freezegrps, freezedim, cos-acceleration, deform)
57 <li><A HREF="#ef"><b>Electric fields</b></A> (E-x, E-xt, E-y, E-yt, E-z, E-zt )
58 <li><A HREF="#qmmm"><b>Mixed quantum/classical dynamics</b></A> (QMMM, QMMM-grps, QMMMscheme, QMmethod, QMbasis, QMcharge, Qmmult, CASorbitals, CASelectrons, SH)
59 <li><A HREF="#gbsa"><b>Implicit solvent</b></A> (implicit-solvent, gb-algorithm, nstgbradii, rgbradii, gb-epsilon-solvent, gb-saltconc, gb-obc-alpha, gb-obc-beta, gb-obc-gamma, gb-dielectric-offset, sa-algorithm, sa-surface-tension)
60 <li><A HREF="#adress"><b>AdResS settings</b></A> (adress, adress_type, adress_const_wf, adress_ex_width, adress_hy_width, adress_ex_forcecap, adress_interface_correction, adress_site, adress_reference_coords, adress_tf_grp_names, adress_cg_grp_names)
61 <li><A HREF="#user"><b>User defined thingies</b></A> (user1-grps, user2-grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
62 <li><A HREF="#idx"><b>Index</b></A>
68 <A NAME="general"><br>
72 Default values are given in parentheses. The first option in
73 the list is always the default option. Units are given in
74 square brackets The difference between a dash and an underscore
78 A <a href="mdp.html">sample <TT>.mdp</TT> file</a> is
79 available. This should be appropriate to start a normal
80 simulation. Edit it to suit your specific needs and desires. </P>
84 <h3>Preprocessing</h3>
87 <dt><b>include:</b></dt>
88 <dd>directories to include in your topology. Format:
89 <PRE>-I/home/john/mylib -I../otherlib</PRE></dd>
90 <dt><b>define:</b></dt>
91 <dd>defines to pass to the preprocessor, default is no defines. You can use
92 any defines to control options in your customized topology files. Options
93 that are already available by default are:
96 <dd>Will tell <tt>grompp</tt> to include flexible water in stead of rigid water into your
97 topology, this can be useful for normal mode analysis.</dd>
99 <dd>Will tell <tt>grompp</tt> to include posre.itp into your topology, used for
100 <!--Idx-->position restraint<!--EIdx-->s.</dd>
109 <dt><b>integrator:</b> (Despite the name, this list includes algorithms that are not actually integrators. <tt>steep</tt> and all entries following it are in this category)</dt>
112 <dd>A leap-frog algorithm<!--QuietIdx-->leap-frog integrator<!--EQuietIdx-->
113 for integrating Newton's equations of motion.</dd>
114 <dt><b>md-vv</b></dt>
115 <dd>A velocity Verlet algorithm for integrating Newton's equations of motion.
116 For constant NVE simulations started from corresponding points in the same trajectory, the trajectories
117 are analytically, but not binary, identical to the <b>md</b> leap-frog integrator. The the kinetic
118 energy, which is determined from the whole step velocities and is therefore
119 slightly too high. The advantage of this integrator is more accurate,
120 reversible Nose-Hoover and Parrinello-Rahman coupling integration
121 based on Trotter expansion, as well as (slightly too small) full step velocity
122 output. This all comes at the cost off extra computation, especially with
123 constraints and extra communication in parallel. Note that for nearly all
124 production simulations the <b>md</b> integrator is accurate enough.
126 <dt><b>md-vv-avek</b></dt>
127 <dd>A velocity Verlet algorithm identical to <b>md-vv</b>, except that
128 the kinetic energy is determined as the average of
129 the two half step kinetic energies as in the <b>md</b> integrator, and this thus more accurate.
130 With Nose-Hoover and/or Parrinello-Rahman coupling this comes with
131 a slight increase in computational cost.
134 <dd> An accurate leap-frog stochastic dynamics integrator.
135 Four Gaussian random number are required
136 per integration step per degree of freedom. With constraints,
137 coordinates needs to be constrained twice per integration step.
138 Depending on the computational cost of the force calculation,
139 this can take a significant part of the simulation time.
140 The temperature for one or more groups of atoms
141 (<b><A HREF="#tc">tc-grps</A></b>)
142 is set with <b><A HREF="#tc">ref-t</A></b> [K],
143 the inverse friction constant for each group is set with
144 <b><A HREF="#tc">tau-t</A></b> [ps].
145 The parameter <b><A HREF="#tc">tcoupl</A></b> is ignored.
146 The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.
147 When used as a thermostat, an appropriate value for <b>tau-t</b> is 2 ps,
148 since this results in a friction that is lower than the internal friction
149 of water, while it is high enough to remove excess heat
150 (unless <b>cut-off</b> or <b>reaction-field</b> electrostatics is used).
151 NOTE: temperature deviations decay twice as fast as with
152 a Berendsen thermostat with the same <b>tau-t</b>.</dd>
154 <dd> An efficient leap-frog stochastic dynamics integrator.
155 This integrator is equivalent to <b>sd</b>, except that it requires
156 only one Gaussian random number and one constraint step and is therefore
157 significantly faster. Without constraints the accuracy is the same as <b>sd</b>.
158 With constraints the accuracy is significantly reduced, so then <b>sd</b>
159 will often be preferred.</dd>
161 <dd>An Euler integrator for Brownian or position Langevin dynamics, the
162 velocity is the force divided by a friction coefficient
163 (<b><A HREF="#ld">bd-fric</A></b> [amu ps<sup>-1</sup>])
164 plus random thermal noise (<b><A HREF="#tc">ref-t</A></b>).
165 When <b><A HREF="#ld">bd-fric</A></b><tt>=0</tt>, the friction coefficient for each
166 particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>, as for the
167 integrator <tt>sd</tt>.
168 The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.</dd>
170 <dt><b>steep</b></dt>
171 <dd>A <!--Idx-->steepest descent<!--EIdx--> algorithm for energy
172 minimization. The maximum step size is <b><A HREF="#em">emstep</A></b>
173 [nm], the tolerance is <b><A HREF="#em">emtol</A></b> [kJ
174 mol<sup>-1</sup> nm<sup>-1</sup>].</dd>
176 <dd>A <!--Idx-->conjugate gradient<!--EIdx--> algorithm for energy
177 minimization, the tolerance is <b>emtol</b> [kJ mol<sup>-1</sup>
178 nm<sup>-1</sup>]. CG is more efficient when a steepest descent step
179 is done every once in a while, this is determined by
180 <b><A HREF="#em">nstcgsteep</A></b>.
181 For a minimization prior to a normal mode analysis, which requires
182 a very high accuracy, GROMACS should be compiled in double precision.</dd>
183 <dt><b>l-bfgs</b></dt>
184 <dd>A <!--Idx-->quasi-Newtonian<!--EIdx--> algorithm for energy minimization
185 according to the low-memory Broyden-Fletcher-Goldfarb-Shanno approach.
186 In practice this seems to converge faster than Conjugate Gradients, but due
187 to the correction steps necessary it is not (yet) parallelized.
190 <dd>Normal mode analysis<!--QuietIdx-->normal-mode analysis<!--EQuietIdx--> is performed
191 on the structure in the <tt>tpr</tt> file. GROMACS should be
192 compiled in double precision.</dd>
194 <dd> Test particle insertion. The last molecule in the topology
195 is the test particle. A trajectory should be provided with
196 the <tt>-rerun</tt> option of <tt>mdrun</tt>. This trajectory
197 should not contain the molecule to be inserted. Insertions
198 are performed <b>nsteps</b> times in each frame at random locations
199 and with random orientiations of the molecule. When <b>nstlist</b>
200 is larger than one, <b>nstlist</b> insertions are performed
201 in a sphere with radius <b><A HREF="#tpi">rtpi</A></b>
202 around a the same random location using the same neighborlist
203 (and the same long-range energy when <b>rvdw</b> or <b>rcoulomb</b>><b>rlist</b>,
204 which is only allowed for single-atom molecules).
205 Since neighborlist construction is expensive, one can perform several
206 extra insertions with the same list almost for free.
207 The random seed is set with <b><A HREF="#ld">ld-seed</A></b>.
208 The temperature for the Boltzmann weighting is set with
209 <b><A HREF="#tc">ref-t</A></b>, this should match the temperature
210 of the simulation of the original trajectory.
211 Dispersion correction is implemented correctly for tpi.
212 All relevant quantities are written to the file specified with
213 the <tt>-tpi</tt> option of <tt>mdrun</tt>.
214 The distribution of insertion energies is written to the file specified with
215 the <tt>-tpid</tt> option of <tt>mdrun</tt>.
216 No trajectory or energy file is written.
217 Parallel tpi gives identical results to single node tpi.
218 For charged molecules, using PME with a fine grid is most accurate
219 and also efficient, since the potential in the system only needs
220 to be calculated once per frame.
223 <dd> Test particle insertion into a predefined cavity location.
224 The procedure is the same as for <b>tpi</b>, except that one coordinate
225 extra is read from the trajectory, which is used as the insertion location.
226 The molecule to be inserted should be centered at 0,0,0. Gromacs does
227 not do this for you, since for different situations a different
228 way of centering might be optimal.
229 Also <b><A HREF="#tpi">rtpi</A></b> sets the radius for the sphere
230 around this location. Neighbor searching is done only once per frame,
231 <b>nstlist</b> is not used.
232 Parallel tpic gives identical results to single node tpic.
235 <dt><b>tinit: (0) [ps]</b></dt>
236 <dd>starting time for your run (only makes sense for integrators <tt>md</tt>,
237 <tt>sd</tt> and <tt>bd</tt>)</dd>
238 <dt><b>dt: (0.001) [ps]</b></dt></dd>
239 <dd>time step for integration (only makes sense for integrators <tt>md</tt>,
240 <tt>sd</tt> and <tt>bd</tt>)</dd>
241 <dt><b>nsteps: (0)</b></dt>
242 <dd>maximum number of steps to integrate or minimize, -1 is no maximum</dd>
243 <dt><b>init-step: (0)</b></dt>
244 <dd>The starting step.
245 The time at an step i in a run is calculated as: t = <tt>tinit</tt> + <tt>dt</tt>*(<tt>init-step</tt> + i).
246 The free-energy lambda is calculated as: lambda = <tt>init-lambda</tt> + <tt>delta-lambda</tt>*(<tt>init-step</tt> + i).
247 Also non-equilibrium MD parameters can depend on the step number.
248 Thus for exact restarts or redoing part of a run it might be necessary to
249 set <tt>init-step</tt> to the step number of the restart frame.
250 <tt>tpbconv</tt> does this automatically.
252 <dt><b>comm-mode:</b></dt>
254 <dt><b>Linear</b></dt>
255 <dd>Remove center of mass translation</dd>
256 <dt><b>Angular</b></dt>
257 <dd>Remove center of mass translation and rotation around the center of mass
260 <dd>No restriction on the center of mass motion
262 <dt><b>nstcomm: (100) [steps]</b></dt>
263 <dd>frequency for center of mass motion removal</dd>
264 <dt><b>comm-grps:</b></dt>
265 <dd>group(s) for center of mass motion removal, default is the whole system</dd>
270 <h3><!--Idx-->Langevin dynamics<!--EIdx--></h3>
273 <dt><b>bd-fric: (0) [amu ps<sup>-1</sup>]</b></dt>
274 <dd>Brownian dynamics friction coefficient.
275 When <b>bd-fric</b><tt>=0</tt>, the friction coefficient for each
276 particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>.</dd>
277 <dt><b>ld-seed: (1993) [integer]</b></dt>
278 <dd>used to initialize random generator for thermal noise
279 for stochastic and Brownian dynamics.
280 When <b>ld-seed</b> is set to -1, the seed is calculated from the process ID.
281 When running BD or SD on multiple processors, each processor uses a seed equal
282 to <b>ld-seed</b> plus the processor number.</dd>
287 <h3>Energy minimization<!--QuietIdx-->energy minimization<!--EQuietIdx--></h3>
289 <dt><b>emtol: (10.0) [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
290 <dd>the minimization is converged when the maximum force is smaller than
292 <dt><b>emstep: (0.01) [nm]</b></dt>
293 <dd>initial step-size</dd>
294 <dt><b>nstcgsteep: (1000) [steps]</b></dt>
295 <dd>frequency of performing 1 steepest descent step while doing
296 conjugate gradient energy minimization.</dd>
297 <dt><b>nbfgscorr: (10)</b></dt>
298 <dd>Number of correction steps to use for L-BFGS minimization. A higher
299 number is (at least theoretically) more accurate, but slower.</dd>
302 <A NAME="xmdrun"><br>
304 <h3>Shell Molecular Dynamics<!--QuietIdx-->shell molecular dynamics<!--EQuietIdx--></h3>
306 flexible constraints are present in the system the positions of the shells
307 and the lengths of the flexible constraints are optimized at
308 every time step until either the RMS force on the shells and constraints
309 is less than emtol, or a maximum number of iterations (niter) has been reached
311 <dt><b>emtol: (10.0) [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
312 <dd>the minimization is converged when the maximum force is smaller than
313 this value. For shell MD this value should be 1.0 at most, but since the
314 variable is used for energy minimization as well the default is 10.0.</dd>
315 <dt><b>niter: (20)</b></dt>
316 <dd>maximum number of iterations for optimizing the shell positions
317 and the flexible constraints.</dd>
318 <dt><b>fcstep: (0) [ps<sup>2</sup>]</b></dt>
319 <dd>the step size for optimizing the flexible constraints.
320 Should be chosen as mu/(d<sup>2</sup>V/dq<sup>2</sup>)
321 where mu is the reduced mass of two particles in a flexible constraint
322 and d<sup>2</sup>V/dq<sup>2</sup> is the second derivative of the potential
323 in the constraint direction. Hopefully this number does not differ too
324 much between the flexible constraints, as the number of iterations
325 and thus the runtime is very sensitive to <tt>fcstep</tt>.
326 Try several values!</dd>
331 <h3>Test particle insertion</h3>
333 <dt><b>rtpi: (0.05) [nm]</b></dt>
334 <dd>the test particle insertion radius see integrators
335 <b><a href="#run">tpi</a></b> and <b><a href="#run">tpic</a></b></dd>
340 <h3>Output control</h3>
342 <dt><b>nstxout: (0) [steps]</b></dt>
343 <dd>frequency to write coordinates to output
344 <!--Idx-->trajectory file<!--EIdx-->, the last coordinates are always written</dd>
345 <dt><b>nstvout: (0) [steps]</b></dt>
346 <dd>frequency to write velocities to output trajectory,
347 the last velocities are always written</dd>
348 <dt><b>nstfout: (0) [steps]</b></dt>
349 <dd>frequency to write forces to output trajectory.</dd>
350 <dt><b>nstlog: (1000) [steps]</b></dt>
351 <dd>frequency to write energies to <!--Idx-->log file<!--EIdx-->,
352 the last energies are always written</dd>
353 <dt><b>nstcalcenergy: (100)</b></dt>
354 <dd>frequency for calculating the energies, 0 is never.
355 This option is only relevant with dynamics.
356 With a twin-range cut-off setup <b>nstcalcenergy</b> should be equal to
357 or a multiple of <b>nstlist</b>.
358 This option affects the performance in parallel simulations,
359 because calculating energies requires global communication between all
360 processes which can become a bottleneck at high parallelization.
362 <dt><b>nstenergy: (1000) [steps]</b></dt>
363 <dd>frequency to write energies to energy file,
364 the last energies are always written,
365 should be a multiple of <b>nstcalcenergy</b>.
366 Note that the exact sums and fluctuations over all MD steps
367 modulo <b>nstcalcenergy</b> are stored in the energy file,
368 so <tt>g_energy</tt> can report exact
369 energy averages and fluctuations also when <b>nstenergy</b><tt>>1</tt></dd>
370 <dt><b>nstxtcout: (0) [steps]</b></dt>
371 <dd>frequency to write coordinates to xtc trajectory</dd>
372 <dt><b>xtc-precision: (1000) [real]</b></dt>
373 <dd>precision to write to xtc trajectory</dd>
374 <dt><b>xtc-grps:</b></dt>
375 <dd>group(s) to write to xtc trajectory, default the whole system is written
376 (if <b>nstxtcout</b> > 0)</dd>
377 <dt><b>energygrps:</b></dt>
378 <dd>group(s) to write to energy file</dd>
383 <h3>Neighbor searching<!--QuietIdx-->neighbor searching<!--EQuietIdx--></h3>
385 <dt><b>cutoff-scheme:</b></dt>
387 <dt><b>group</b></dt>
388 <dd>Generate a pair list for groups of atoms. These groups correspond to the
389 charge groups in the topology. This was the only cut-off treatment scheme
391 There is no explicit buffering of the pair list. This enables efficient force
392 calculations, but energy is only conserved when a buffer is explicitly added.
393 For energy conservation, the <b>Verlet</b> option provides a more convenient
394 and efficient algorithm.</dd>
396 <dt><b>Verlet</b></dt>
397 <dd>Generate a pair list with buffering. The buffer size is automatically set
398 based on <b>verlet-buffer-drift</b>, unless this is set to -1, in which case
399 <b>rlist</b> will be used. This option has an explicit, exact cut-off at
400 <b>rvdw</b>=<b>rcoulomb</b>. Currently only cut-off, reaction-field,
401 PME electrostatics and plain LJ are supported. Some <tt>mdrun</tt> functionality
402 is not yet supported with the <b>Verlet</b> scheme, but <tt>grompp</tt> checks for this.
403 Native GPU acceleration is only supported with <b>Verlet</b>. With GPU-accelerated PME,
404 <tt>mdrun</tt> will automatically tune the CPU/GPU load balance by
405 scaling <b>rcoulomb</b> and the grid spacing. This can be turned off with
408 <b>Verlet</b> is somewhat faster than <b>group</b> when there is no water, or if <b>group</b> would use a pair-list buffer to conserve energy.
412 <dt><b>nstlist: (10) [steps]</b></dt>
414 <dt><b>>0</b></dt>
415 <dd>Frequency to update the <!--Idx-->neighbor list<!--EIdx--> (and
416 the long-range forces, when using twin-range cut-offs). When this is 0,
417 the neighbor list is made only once.
418 With energy minimization the neighborlist will be updated for every
419 energy evaluation when <b>nstlist</b><tt>>0</tt>.
420 With non-bonded force calculation on the GPU, a value of 20 or more gives
421 the best performance.</dd>
423 <dd>The neighbor list is only constructed once and never updated.
424 This is mainly useful for vacuum simulations in which all particles
427 <dd>Automated update frequency, only supported with <b>cutoff-scheme</b>=<b>group</b>.
428 This can only be used with switched, shifted or user potentials where
429 the cut-off can be smaller than <b>rlist</b>. One then has a buffer
430 of size <b>rlist</b> minus the longest cut-off.
431 The neighbor list is only updated when one or more particles have moved further
432 than half the buffer size from the center of geometry of their charge group
433 as determined at the previous neighbor search.
434 Coordinate scaling due to pressure coupling or the <b>deform</b> option
435 is taken into account.
436 This option guarantees that their are no cut-off artifacts,
437 but for larger systems this can come at a high computational cost,
438 since the neighbor list update frequency will be determined
439 by just one or two particles moving slightly beyond the half buffer length
440 (which does not necessarily imply that the neighbor list is invalid),
441 while 99.99% of the particles are fine.
445 <dt><b>nstcalclr: (-1) [steps]</b></dt>
447 Controls the period between calculations of long-range forces when
448 using the group cut-off scheme.
451 <dd>Calculate the long-range forces every single step. This is useful
452 to have separate neighbor lists with buffers for electrostatics and Van
453 der Waals interactions, and in particular it makes it possible to have
454 the Van der Waals cutoff longer than electrostatics (useful e.g. with
455 PME). However, there is no point in having identical long-range
456 cutoffs for both interaction forms and update them every step - then
457 it will be slightly faster to put everything in the short-range
459 <dt><b>>1</b></dt>
460 <dd>Calculate the long-range forces every <b>nstcalclr</b> steps and
461 use a multiple-time-step integrator to combine forces. This can now be
462 done more frequently than <b>nstlist</b> since the lists are stored,
463 and it might be a good idea e.g. for Van der Waals interactions that
464 vary slower than electrostatics.</dd>
466 <dd>Calculate long-range forces on steps where neighbor searching is
467 performed. While this is the default value, you might want to consider
468 updating the long-range forces more frequently.</dd>
470 Note that twin-range force evaluation might be enabled automatically
471 by PP-PME load balancing. This is done in order to maintain the chosen
472 Van der Waals interaction radius even if the load balancing is
473 changing the electrostatics cutoff. If the <tt>.mdp</tt> file already
474 specifies twin-range interactions (e.g. to evaluate Lennard-Jones
475 interactions with a longer cutoff than the PME electrostatics every
476 2-3 steps), the load balancing will have also a small effect on
477 Lennard-Jones, since the short-range cutoff (inside which forces are
478 evaluated every step) is changed.
483 <dt><b>ns-type:</b></dt>
486 <dd>Make a grid in the box and only check atoms in neighboring grid
487 cells when constructing a new neighbor list every <b>nstlist</b> steps.
488 In large systems grid search is much faster than simple search.</dd>
489 <dt><b>simple</b></dt>
490 <dd>Check every atom in the box when constructing a new neighbor list
491 every <b>nstlist</b> steps.</dd>
497 <dd>Use periodic boundary conditions in all directions.</dd>
499 <dd>Use no periodic boundary conditions, ignore the box.
500 To simulate without cut-offs, set all cut-offs to 0 and <b>nstlist</b><tt>=0</tt>.
501 For best performance without cut-offs, use <b>nstlist</b><tt>=0</tt>,
502 <b>ns-type</b><tt>=simple</tt>
503 and particle decomposition instead of domain decomposition.</dd>
505 <dd>Use periodic boundary conditions in x and y directions only.
506 This works only with <b>ns-type</b><tt>=grid</tt> and can be used
507 in combination with <b><a href="#walls">walls</a></b>.
508 Without walls or with only one wall the system size is infinite
509 in the z direction. Therefore pressure coupling or Ewald summation
510 methods can not be used.
511 These disadvantages do not apply when two walls are used.</dd>
514 <dt><b>periodic-molecules:</b></dt>
517 <dd>molecules are finite, fast molecular PBC can be used</dd>
519 <dd>for systems with molecules that couple to themselves through
520 the periodic boundary conditions, this requires a slower PBC algorithm
521 and molecules are not made whole in the output</dd>
524 <dt><b>verlet-buffer-drift: (0.005) [kJ/mol/ps]</b></dt>
525 <dd>Useful only with <b>cutoff-scheme</b>=<b>Verlet</b>. This sets the target energy drift
526 per particle caused by the Verlet buffer, which indirectly sets <b>rlist</b>.
527 As both <b>nstlist</b> and the Verlet buffer size are fixed
528 (for performance reasons), particle pairs not in the pair list can occasionally
529 get within the cut-off distance during <b>nstlist</b>-1 nsteps. This
530 generates energy drift. In a constant-temperature ensemble, the drift can be
531 estimated for a given cut-off and <b>rlist</b>. The estimate assumes a
532 homogeneous particle distribution, hence the drift might be slightly
533 underestimated for multi-phase systems. For longer pair-list life-time
534 (<b>nstlist</b>-1)*dt the drift is overestimated, because the interactions
535 between particles are ignored. Combined with cancellation of errors,
536 the actual energy drift is usually one to two orders of magnitude smaller.
537 Note that the generated buffer size takes into account that
538 the GROMACS pair-list setup leads to a reduction in the drift by
539 a factor 10, compared to a simple particle-pair based list.
540 Without dynamics (energy minimization etc.), the buffer is 5% of the cut-off.
541 For dynamics without temperature coupling or to override the buffer size,
542 use <b>verlet-buffer-drift</b>=-1 and set <b>rlist</b> manually.</dd>
544 <dt><b>rlist: (1) [nm]</b></dt>
545 <dd>Cut-off distance for the short-range neighbor list.
546 With <b>cutoff-scheme</b>=<b>Verlet</b>, this is by default set by the
547 <b>verlet-buffer-drift</b> option and the value of <b>rlist</b> is ignored.</dd>
549 <dt><b>rlistlong: (-1) [nm]</b></dt>
550 <dd>Cut-off distance for the long-range neighbor list.
551 This parameter is only relevant for a twin-range cut-off setup
552 with switched potentials. In that case a buffer region is required to account
553 for the size of charge groups. In all other cases this parameter
554 is automatically set to the longest cut-off distance.</dd>
560 <h3>Electrostatics<!--QuietIdx-->electrostatics<!--EQuietIdx--></h3>
562 <dt><b>coulombtype:</b></dt>
565 <dt><b>Cut-off</b></dt>
566 <dd>Twin range cut-offs with neighborlist cut-off <b>rlist</b> and
567 Coulomb cut-off <b>rcoulomb</b>,
568 where <b>rcoulomb</b>≥<b>rlist</b>.
570 <dt><b>Ewald</b></dt>
571 <dd>Classical <!--Idx-->Ewald sum<!--EIdx--> electrostatics.
572 The real-space cut-off <b>rcoulomb</b> should be equal to <b>rlist</b>.
573 Use e.g. <b>rlist</b><tt>=0.9</tt>, <b>rcoulomb</b><tt>=0.9</tt>. The highest magnitude of
574 wave vectors used in reciprocal space is controlled by <b>fourierspacing</b>.
575 The relative accuracy of direct/reciprocal space
576 is controlled by <b>ewald-rtol</b>.
578 NOTE: Ewald scales as O(N<sup>3/2</sup>)
579 and is thus extremely slow for large systems. It is included mainly for
580 reference - in most cases PME will perform much better.</dd>
582 <dt><b><!--Idx-->PME<!--EIdx--></b></dt>
583 <dd>Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct space is similar
584 to the Ewald sum, while the reciprocal part is performed with
585 FFTs. Grid dimensions are controlled with <b>fourierspacing</b> and the
586 interpolation order with <b>pme-order</b>. With a grid spacing of 0.1
587 nm and cubic interpolation the electrostatic forces have an accuracy
588 of 2-3*10<sup>-4</sup>. Since the error from the vdw-cutoff is larger than this you
589 might try 0.15 nm. When running in parallel the interpolation
590 parallelizes better than the FFT, so try decreasing grid dimensions
591 while increasing interpolation.</dd>
593 <dt><b><!--Idx-->P3M-AD<!--EIdx--></b></dt>
594 <dd>Particle-Particle Particle-Mesh algorithm with analytical derivative
595 for for long range electrostatic interactions. The method and code
596 is identical to SPME, except that the influence function is optimized
597 for the grid. This gives a slight increase in accuracy.</dd>
599 <dt><b>Reaction-Field electrostatics<!--QuietIdx-->reaction-field electrostatics<!--EQuietIdx--></b></dt>
600 <dd>Reaction field with Coulomb cut-off <b>rcoulomb</b>,
601 where <b>rcoulomb</b> ≥ <b>rlist</b>.
602 The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
603 The dielectric constant can be set to infinity by setting <b>epsilon-rf</b><tt>=0</tt>.</dd>
605 <dt><b>Generalized-Reaction-Field</b></dt>
606 <dd>Generalized reaction field with Coulomb cut-off <b>rcoulomb</b>,
607 where <b>rcoulomb</b> ≥ <b>rlist</b>.
608 The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
609 The ionic strength is computed from the number of charged
610 (i.e. with non zero charge) <!--Idx-->charge group<!--EIdx-->s.
611 The temperature for the GRF potential is set with
612 <b><A HREF="#tc">ref-t</A></b> [K].</dd>
614 <dt><b>Reaction-Field-zero</b></dt>
615 <dd>In GROMACS, normal reaction-field electrostatics with
616 <b>cutoff-scheme</b><b>=group</b> leads to bad
617 energy conservation. <b>Reaction-Field-zero</b> solves this
618 by making the potential zero beyond the cut-off. It can only
619 be used with an infinite dielectric constant (<b>epsilon-rf=0</b>),
620 because only for that value the force vanishes at the cut-off.
621 <b>rlist</b> should be 0.1 to 0.3 nm larger than <b>rcoulomb</b>
622 to accommodate for the size of charge groups and diffusion
623 between neighbor list updates. This, and the fact that table lookups
624 are used instead of analytical functions make <b>Reaction-Field-zero</b>
625 computationally more expensive than normal reaction-field.</dd>
627 <dt><b>Reaction-Field-nec</b></dt>
628 <dd>The same as <b>Reaction-Field</b>, but implemented as in
629 GROMACS versions before 3.3. No reaction-field correction is applied
630 to excluded atom pairs and self pairs.
631 The 1-4 interactions are calculated using a reaction-field.
632 The missing correction due to the excluded pairs that do not have a 1-4
633 interaction is up to a few percent of the total electrostatic
634 energy and causes a minor difference in the forces and the pressure.</dd>
636 <dt><b>Shift</b></dt>
637 <dd>Analogous to <b>Shift</b> for <b>vdwtype</b>.
638 You might want to use <b>Reaction-Field-zero</b> instead,
639 which has a similar potential shape, but has a physical interpretation
640 and has better energies due to the exclusion correction terms.
643 <dt><b>Encad-Shift</b></dt>
645 potential is decreased over the whole range, using the definition
646 from the Encad simulation package.</dd>
648 <dt><b>Switch</b></dt>
649 <dd>Analogous to <b>Switch</b> for <b>vdwtype</b>.
650 Switching the Coulomb potential can lead to serious artifacts,
651 advice: use <b>Reaction-Field-zero</b> instead.</dd>
654 <dd><a name="usertab"></a><tt>mdrun</tt> will now expect to find a file
655 <tt>table.xvg</tt> with user-defined potential functions for
656 repulsion, dispersion and Coulomb. When pair interactions are present,
657 <tt>mdrun</tt> also expects to find a file <tt>tablep.xvg</tt> for
658 the pair interactions. When the same interactions should be used
659 for non-bonded and pair interactions the user can specify the same
660 file name for both table files.
661 These files should contain 7
662 columns: the <tt>x</tt> value,
663 <tt>f(x)</tt>, <tt>-f'(x)</tt>,
664 <tt>g(x)</tt>, <tt>-g'(x)</tt>,
665 <tt>h(x)</tt>, <tt>-h'(x)</tt>,
666 where <tt>f(x)</tt> is the Coulomb function, <tt>g(x)</tt> the dispersion function
667 and <tt>h(x)</tt> the repulsion function.
668 When <b>vdwtype</b> is not set to <b>User</b> the values
669 for <tt>g</tt>, <tt>-g'</tt>, <tt>h</tt> and <tt>-h'</tt> are ignored.
670 For the non-bonded interactions <tt>x</tt> values should run
671 from 0 to the largest cut-off distance + <b>table-extension</b>
672 and should be uniformly spaced. For the pair interactions the table
673 length in the file will be used.
674 The optimal spacing, which is used for non-user tables,
675 is <tt>0.002</tt> [nm] when you run in single precision
676 or <tt>0.0005</tt> [nm] when you run in double precision.
677 The function value at <tt>x=0</tt> is not important. More information is
678 in the printed manual.</dd>
680 <dt><b>PME-Switch</b></dt>
681 <dd>A combination of PME and a switch function for the direct-space part
682 (see above). <b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
683 This is mainly useful constant energy simulations (note that using
684 <b>PME</b> with <b>cutoff-scheme</b>=<b>Verlet</b> will be more efficient).
687 <dt><b>PME-User</b></dt>
688 <dd>A combination of PME and user tables (see above).
689 <b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
690 The PME mesh contribution is subtracted from the user table by <tt>mdrun</tt>.
691 Because of this subtraction the user tables should contain
692 about 10 decimal places.</dd>
694 <dt><b>PME-User-Switch</b></dt>
695 <dd>A combination of PME-User and a switching function (see above).
696 The switching function is applied to final particle-particle interaction,
697 i.e. both to the user supplied function and the PME Mesh correction part.</dd>
701 <dt><b>coulomb-modifier:</b></dt>
703 <dt><b>Potential-shift-Verlet</b></dt>
704 <dd>Selects <b>Potential-shift</b> with the Verlet cutoff-scheme,
705 as it is (nearly) free; selects <b>None</b> with the group cutoff-scheme.</dd>
706 <dt><b>Potential-shift</b></dt>
707 <dd>Shift the Coulomb potential by a constant such that it is zero at the cut-off.
708 This makes the potential the integral of the force. Note that this does not
709 affect the forces or the sampling.</dd>
711 <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>
716 <dt><b>rcoulomb-switch: (0) [nm]</b></dt>
717 <dd>where to start switching the Coulomb potential</dd>
719 <dt><b>rcoulomb: (1) [nm]</b></dt>
720 <dd>distance for the Coulomb <!--Idx-->cut-off<!--EIdx--></dd>
722 <dt><b>epsilon-r: (1)</b></dt>
723 <dd>The relative <!--Idx-->dielectric constant<!--EIdx-->.
724 A value of 0 means infinity.</dd>
726 <dt><b>epsilon-rf: (0)</b></dt>
727 <dd>The relative dielectric constant of the reaction field.
728 This is only used with reaction-field electrostatics.
729 A value of 0 means infinity.</dd>
736 <dt><b>vdwtype:</b></dt>
738 <dt><b>Cut-off</b></dt>
739 <dd>Twin range cut-offs with neighbor list cut-off <b>rlist</b> and
740 VdW cut-off <b>rvdw</b>,
741 where <b>rvdw</b> <tt>≥</tt> <b>rlist</b>.</dd>
742 <dt><b>Shift</b></dt>
743 <dd>The LJ (not Buckingham) potential is decreased over the whole
744 range and the forces decay smoothly to zero between <b>rvdw-switch</b>
745 and <b>rvdw</b>. The neighbor search cut-off <b>rlist</b> should be
746 0.1 to 0.3 nm larger than <b>rvdw</b> to accommodate for the size of
747 charge groups and diffusion between neighbor list
750 <dt><b>Switch</b></dt>
751 <dd>The LJ (not Buckingham)
752 potential is normal out to <b>rvdw-switch</b>, after which it is switched
753 off to reach zero at <b>rvdw</b>. Both the potential and force functions
754 are continuously smooth, but be aware that all switch functions will give rise
755 to a bulge (increase) in the force (since we are switching the potential).
756 The neighbor search cut-off <b>rlist</b> should be 0.1 to 0.3 nm larger than
757 <b>rvdw</b> to accommodate for the size of charge groups and diffusion
758 between neighbor list updates.</dd>
760 <dt><b>Encad-Shift</b></dt>
761 <dd>The LJ (not Buckingham)
762 potential is decreased over the whole range, using the definition
763 from the Encad simulation package.</dd>
766 <dd>See <b><a href="#usertab">user</a></b> for <b>coulombtype</b>.
767 The function value at <tt>x=0</tt> is not important. When you want to
768 use LJ correction, make sure that <b>rvdw</b> corresponds to the
769 cut-off in the user-defined function.
770 When <b>coulombtype</b> is not set to <b>User</b> the values
771 for <tt>f</tt> and <tt>-f'</tt> are ignored.</dd>
774 <dt><b>vdw-modifier:</b></dt>
776 <dt><b>Potential-shift-Verlet</b></dt>
777 <dd>Selects <b>Potential-shift</b> with the Verlet cutoff-scheme,
778 as it is (nearly) free; selects <b>None</b> with the group cutoff-scheme.</dd>
779 <dt><b>Potential-shift</b></dt>
780 <dd>Shift the Van der Waals potential by a constant such that it is zero at the cut-off.
781 This makes the potential the integral of the force. Note that this does not
782 affect the forces or the sampling.</dd>
784 <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>
787 <dt><b>rvdw-switch: (0) [nm]</b></dt>
788 <dd>where to start switching the LJ potential</dd>
790 <dt><b>rvdw: (1) [nm]</b></dt>
791 <dd>distance for the LJ or Buckingham <!--Idx-->cut-off<!--EIdx--></dd>
793 <dt><b>DispCorr:</b></dt>
794 <dd><dl compact></dd>
796 <dd>don't apply any correction</dd>
797 <dt><b>EnerPres</b></dt>
798 <dd>apply long range <!--Idx-->dispersion correction<!--EIdx-->s for Energy
801 <dd>apply long range dispersion corrections for Energy
810 <dt><b>table-extension: (1) [nm]</b></dt>
811 <dd>Extension of the non-bonded potential lookup tables beyond the largest cut-off distance.
812 The value should be large enough to account for charge group sizes
813 and the diffusion between neighbor-list updates.
814 Without user defined potential the same table length is used
815 for the lookup tables for the 1-4 interactions,
816 which are always tabulated irrespective of the use of
817 tables for the non-bonded interactions. </dd>
819 <dt><b>energygrp-table:</b></dt>
820 <dd>When user tables are used for electrostatics and/or VdW,
821 here one can give pairs of energy groups for which seperate
822 user tables should be used.
823 The two energy groups will be appended to the table file name,
824 in order of their definition in <b>energygrps</b>, seperated by underscores.
825 For example, if <tt>energygrps = Na Cl Sol</tt>
826 and <tt>energygrp-table = Na Na Na Cl</tt>, <tt>mdrun</tt> will read
827 <tt>table_Na_Na.xvg</tt> and <tt>table_Na_Cl.xvg</tt> in addition
828 to the normal <tt>table.xvg</tt> which will be used for all other
837 <dt><b>fourierspacing: (0.12) [nm]</b></dt>
838 <dd>For ordinary Ewald, the ratio of the box dimensions and the spacing
839 determines a lower bound for the number of wave vectors to use in each
840 (signed) direction. For PME and P3M, that ratio determines a lower bound
841 for the number of Fourier-space grid points that will be used along that
842 axis. In all cases, the number for each direction can be overridden by
843 entering a non-zero value for <b>fourier_n[xyz]</b>.
844 For optimizing the relative load of the particle-particle interactions
845 and the mesh part of PME, it is useful to know that
846 the accuracy of the electrostatics remains nearly constant
847 when the Coulomb cut-off and the PME grid spacing are scaled
848 by the same factor.</dd>
850 <dt><b>fourier-nx (0) ; fourier-ny (0) ; fourier-nz: (0)</b></dt>
851 <dd>Highest magnitude of wave vectors in reciprocal space when using Ewald.</dd>
852 <dd>Grid size when using PME or P3M. These values override
853 <b>fourierspacing</b> per direction. The best choice is powers of
854 2, 3, 5 and 7. Avoid large primes.</dd>
856 <dt><b>pme-order (4)</b></dt>
857 <dd>Interpolation order for PME. 4 equals cubic interpolation. You might try
858 6/8/10 when running in parallel and simultaneously decrease grid dimension.</dd>
860 <dt><b>ewald-rtol (1e-5)</b></dt>
861 <dd>The relative strength of the Ewald-shifted direct potential at
862 <b>rcoulomb</b> is given by <b>ewald-rtol</b>.
863 Decreasing this will give a more accurate direct sum,
864 but then you need more wave vectors for the reciprocal sum.</dd>
866 <dt><b>ewald-geometry: (3d)</b></dt>
869 <dd>The Ewald sum is performed in all three dimensions.</dd>
871 <dd>The reciprocal sum is still performed in 3D,
872 but a force and potential correction applied in the <tt>z</tt>
873 dimension to produce a pseudo-2D summation.
874 If your system has a slab geometry in the <tt>x-y</tt> plane you can
875 try to increase the <tt>z</tt>-dimension of the box (a box height of 3 times
876 the slab height is usually ok)
877 and use this option.</dd>
880 <dt><b>epsilon-surface: (0)</b></dt>
881 <dd>This controls the dipole correction to the Ewald summation in 3D. The
882 default value of zero means it is turned off. Turn it on by setting it to the value
883 of the relative permittivity of the imaginary surface around your infinite system. Be
884 careful - you shouldn't use this if you have free mobile charges in your system.
885 This value does not affect the slab 3DC variant of the long range corrections.</dd>
888 <dt><b>optimize-fft:</b></dt>
891 <dd>Don't calculate the optimal FFT plan for the grid at startup.</dd>
893 <dd>Calculate the optimal FFT plan for the grid at startup. This saves a
894 few percent for long simulations, but takes a couple of minutes
902 <h3>Temperature coupling<!--QuietIdx-->temperature coupling<!--EQuietIdx--></h3>
905 <dt><b>tcoupl:</b></dt>
908 <dd>No temperature coupling.</dd>
909 <dt><b>berendsen</b></dt>
910 <dd>Temperature coupling with a Berendsen-thermostat to a bath with
911 temperature <b>ref-t</b> [K], with time constant <b>tau-t</b> [ps].
912 Several groups can be coupled separately, these are specified in the
913 <b>tc-grps</b> field separated by spaces.</dd>
914 <dt><b>nose-hoover</b></dt>
915 <dd>Temperature coupling using a Nose-Hoover extended
916 ensemble. The reference temperature and coupling groups are selected
917 as above, but in this case <b>tau-t</b> [ps] controls the period
918 of the temperature fluctuations at equilibrium, which is slightly
919 different from a relaxation time.
920 For NVT simulations the conserved energy quantity is written
921 to energy and log file.</dd>
922 <dt><b>v-rescale</b></dt>
923 <dd>Temperature coupling using velocity rescaling with a stochastic term
925 This thermostat is similar to Berendsen coupling, with the same scaling
926 using <b>tau-t</b>, but the stochastic term ensures that a proper
927 canonical ensemble is generated. The random seed is set with
928 <b><A HREF="#ld">ld-seed</A></b>.
929 This thermostat works correctly even for <b>tau-t</b><tt>=0</tt>.
930 For NVT simulations the conserved energy quantity is written
931 to the energy and log file.</dd>
933 <dt><b>nsttcouple: (-1)</b></dt>
934 <dd>The frequency for coupling the temperature.
935 The default value of -1 sets <b>nsttcouple</b> equal to <b>nstlist</b>,
936 unless <b>nstlist</b>≤0, then a value of 10 is used.
937 For velocity Verlet integrators <b>nsttcouple</b> is set to 1.</dd>
939 <dt><b>nh-chain-length (10)</b></dt>
940 <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>
941 <dt><b>tc-grps:</b></dt>
942 <dd>groups to couple separately to temperature bath</dd>
943 <dt><b>tau-t: [ps]</b></dt>
944 <dd>time constant for coupling (one for each group in <b>tc-grps</b>),
945 -1 means no temperature coupling</dd>
946 <dt><b>ref-t: [K]</b></dt>
947 <dd>reference temperature for coupling (one for each group in <b>tc-grps</b>)</dd>
952 <h3>Pressure coupling<!--QuietIdx-->pressure coupling<!--EQuietIdx--></h3>
955 <dt><b>pcoupl:</b></dt>
958 <dd>No pressure coupling. This means a fixed box size.</dd>
959 <dt><b>berendsen</b></dt>
960 <dd>Exponential relaxation pressure coupling with time constant
961 <b>tau-p</b> [ps]. The box is scaled every timestep. It has been
962 argued that this does not yield a correct thermodynamic ensemble,
963 but it is the most efficient way to scale a box at the beginning
965 <dt><b>Parrinello-Rahman</b></dt>
966 <dd>Extended-ensemble pressure coupling where the box vectors are
967 subject to an equation of motion. The equation of motion for the atoms
968 is coupled to this. No instantaneous scaling takes place. As for
969 Nose-Hoover temperature coupling the time constant <b>tau-p</b> [ps]
970 is the period of pressure fluctuations at equilibrium. This is
971 probably a better method when you want to apply pressure scaling
972 during data collection, but beware that you can get very large
973 oscillations if you are starting from a different pressure. For
974 simulations where the exact fluctation of the NPT ensemble are
975 important, or if the pressure coupling time is very short it may not
976 be appropriate, as the previous time step pressure is used in some
977 steps of the GROMACS implementation for the current time step pressure.</dd>
980 <dd>Martyna-Tuckerman-Tobias-Klein implementation, only useable with <b>md-vv</b>
981 or <b>md-vv-avek</b>, very similar to Parrinello-Rahman.
982 As for Nose-Hoover temperature coupling the time constant <b>tau-p</b>
983 [ps] is the period of pressure fluctuations at equilibrium. This is
984 probably a better method when you want to apply pressure scaling
985 during data collection, but beware that you can get very large
986 oscillations if you are starting from a different pressure. Currently only supports isotropic scaling.</dd>
990 <dt><b>pcoupltype:</b></dt>
992 <dt><b>isotropic</b></dt>
993 <dd>Isotropic pressure coupling with time constant <b>tau-p</b> [ps].
994 The compressibility and reference pressure are set with
995 <b>compressibility</b> [bar<sup>-1</sup>] and <b>ref-p</b> [bar], one
996 value is needed.</dd>
997 <dt><b>semiisotropic</b></dt>
998 <dd>Pressure coupling which is isotropic in the <tt>x</tt> and <tt>y</tt> direction,
999 but different in the <tt>z</tt> direction.
1000 This can be useful for membrane simulations.
1001 2 values are needed for <tt>x/y</tt> and <tt>z</tt> directions respectively.</dd>
1002 <dt><b>anisotropic</b></dt>
1003 <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>
1004 components, respectively.
1005 When the off-diagonal compressibilities are set to zero,
1006 a rectangular box will stay rectangular.
1007 Beware that anisotropic scaling can lead to extreme deformation
1008 of the simulation box.</dd>
1009 <dt><b>surface-tension</b></dt>
1010 <dd>Surface tension coupling for surfaces parallel to the xy-plane.
1011 Uses normal pressure coupling for the <tt>z</tt>-direction, while the surface tension
1012 is coupled to the <tt>x/y</tt> dimensions of the box.
1013 The first <b>ref-p</b> value is the reference surface tension times
1014 the number of surfaces [bar nm],
1015 the second value is the reference <tt>z</tt>-pressure [bar].
1016 The two <b>compressibility</b> [bar<sup>-1</sup>] values are the compressibility
1017 in the <tt>x/y</tt> and <tt>z</tt> direction respectively.
1018 The value for the <tt>z</tt>-compressibility should be reasonably accurate since it
1019 influences the convergence of the surface-tension, it can also be set to zero
1020 to have a box with constant height.</dd>
1023 <dt><b>nstpcouple: (-1)</b></dt>
1024 <dd>The frequency for coupling the pressure.
1025 The default value of -1 sets <b>nstpcouple</b> equal to <b>nstlist</b>,
1026 unless <b>nstlist</b> ≤0, then a value of 10 is used.
1027 For velocity Verlet integrators <b>nstpcouple</b> is set to 1.</dd>
1030 <dt><b>tau-p: (1) [ps]</b></dt>
1031 <dd>time constant for coupling</dd>
1032 <dt><b>compressibility: [bar<sup>-1</sup>]</b></dt>
1033 <dd>compressibility (NOTE: this is now really in bar<sup>-1</sup>)
1034 For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar<sup>-1</sup>].</dd>
1035 <dt><b>ref-p: [bar]</b></dt>
1036 <dd>reference pressure for coupling</dd>
1037 <dt><b>refcoord-scaling:</b></dt>
1040 <dd>The reference coordinates for position restraints are not modified.
1041 Note that with this option the virial and pressure will depend on the absolute
1042 positions of the reference coordinates.</dd>
1044 <dd>The reference coordinates are scaled with the scaling matrix of the pressure coupling.</dd>
1046 <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.
1053 <h3>Simulated annealing<!--QuietIdx-->simulated annealing<!--EQuietIdx--></h3>
1055 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!
1057 <dt><b>annealing:</b></dt>
1058 <dd>Type of annealing for each temperature group</dd>
1059 <dd><dl compact></dd>
1061 <dd>No simulated annealing - just couple to reference temperature value.</dd>
1062 <dt><b>single</b></dt>
1063 <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>
1064 <dt><b>periodic</b></dt>
1065 <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.
1069 <dt><b>annealing-npoints:</b></dt>
1070 <dd>A list with the number of annealing reference/control points used for
1071 each temperature group. Use 0 for groups that are not annealed. The number of entries should equal the number of temperature groups.</dd>
1073 <dt><b>annealing-time:</b></dt>
1074 <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>
1076 <dt><b>annealing-temp:</b></dt>
1077 <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>
1079 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>.
1080 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!
1085 <h3>Velocity generation</h3>
1088 <dt><b>gen-vel:</b></dt>
1091 <dd> Do not generate velocities. The velocities are set to zero
1092 when there are no velocities in the input structure file.</dd>
1094 <dd>Generate velocities in <tt>grompp</tt> according to a Maxwell distribution at
1095 temperature <b>gen-temp</b> [K], with random seed <b>gen-seed</b>.
1096 This is only meaningful with integrator <b><A HREF="#run">md</A></b>.</dd>
1098 <dt><b>gen-temp: (300) [K]</b></dt>
1099 <dd>temperature for Maxwell distribution</dd>
1100 <dt><b>gen-seed: (173529) [integer]</b></dt>
1101 <dd>used to initialize random generator for random velocities,
1102 when <b>gen-seed</b> is set to -1, the seed is calculated from
1103 the process ID number.
1111 <dt><b>constraints<!--QuietIdx-->constraint algorithms<!--EQuietIdx-->:</b></dt>
1113 <dt><b>none</b></dt>
1114 <dd>No constraints except for those defined explicitly in the topology,
1115 i.e. bonds are represented by a harmonic (or other) potential
1116 or a Morse potential (depending on the setting of <b>morse</b>)
1117 and angles by a harmonic (or other) potential.
1118 <dt><b>h-bonds</b></dt>
1119 <dd>Convert the bonds with H-atoms to constraints.</dd>
1120 <dt><b>all-bonds</b></dt>
1121 <dd>Convert all bonds to constraints.</dd>
1122 <dt><b>h-angles</b></dt>
1123 <dd>Convert all bonds and additionally the angles that involve H-atoms
1124 to bond-constraints.</dd>
1125 <dt><b>all-angles</b></dt>
1126 <dd>Convert all bonds and angles to bond-constraints.</dd>
1129 <dt><b>constraint-algorithm:</b></dt>
1131 <dt><b><!--Idx-->LINCS<!--EIdx--></b></dt>
1132 <dd>LINear Constraint Solver.
1133 With domain decomposition the parallel version P-LINCS is used.
1134 The accuracy in set with
1135 <b>lincs-order</b>, which sets the number of matrices in the expansion
1136 for the matrix inversion.
1137 After the matrix inversion correction the algorithm does
1138 an iterative correction to compensate for lengthening due to rotation.
1139 The number of such iterations can be controlled with
1140 <b>lincs-iter</b>. The root mean square relative constraint deviation
1141 is printed to the log file every <b>nstlog</b> steps.
1142 If a bond rotates more than <b>lincs-warnangle</b> [degrees] in one step,
1143 a warning will be printed both to the log file and to <TT>stderr</TT>.
1144 LINCS should not be used with coupled angle constraints.
1146 <dt><b><!--Idx-->SHAKE<!--EIdx--></b></dt>
1147 <dd>SHAKE is slightly slower and less stable than LINCS, but does work with
1149 The relative tolerance is set with <b>shake-tol</b>, 0.0001 is a good value
1150 for ``normal'' MD. SHAKE does not support constraints between atoms
1151 on different nodes, thus it can not be used with domain decompositon
1152 when inter charge-group constraints are present.
1153 SHAKE can not be used with energy minimization.
1156 <dt><b>continuation:</b></dt>
1157 <dd>This option was formerly known as <tt>unconstrained-start</tt>.</dd>
1160 <dd>apply constraints to the start configuration and reset shells</dd>
1162 <dd>do not apply constraints to the start configuration
1163 and do not reset shells, useful for exact coninuation and reruns</dd>
1167 <dt><b>shake-tol: (0.0001)</b></dt>
1168 <dd>relative tolerance for SHAKE</dd>
1169 <dt><b>lincs-order: (4)</b></dt>
1170 <dd>Highest order in the expansion of the constraint coupling matrix.
1171 When constraints form triangles, an additional expansion of the same
1172 order is applied on top of the normal expansion only for the couplings
1173 within such triangles.
1174 For ``normal'' MD simulations an order of 4 usually suffices, 6 is
1175 needed for large time-steps with virtual sites or BD.
1176 For accurate energy minimization an order of 8 or more might be required.
1177 With domain decomposition, the cell size is limited by the distance
1178 spanned by <b>lincs-order</b>+1 constraints. When one wants to scale
1179 further than this limit, one can decrease <b>lincs-order</b> and increase
1180 <b>lincs-iter</b>, since the accuracy does not deteriorate
1181 when (1+<b>lincs-iter</b>)*<b>lincs-order</b> remains constant.</dd>
1182 <dt><b>lincs-iter: (1)</b></dt>
1183 <dd>Number of iterations to correct for rotational lengthening in LINCS.
1184 For normal runs a single step is sufficient, but for NVE
1185 runs where you want to conserve energy accurately or for accurate
1186 energy minimization you might want to increase it to 2.
1187 <dt><b>lincs-warnangle: </b>(30) [degrees]</dt>
1188 <dd>maximum angle that a bond can rotate before LINCS will complain</dd>
1190 <dt><b>morse:</b></dt>
1193 <dd>bonds are represented by a harmonic potential</dd>
1195 <dd>bonds are represented by a Morse potential</dd>
1199 <A NAME="egexcl"><br>
1201 <h3>Energy group <!--Idx-->exclusions<!--EIdx--></h3>
1203 <dt><b>energygrp-excl: </b></dt>
1204 <dd>Pairs of energy groups for which all non-bonded interactions are
1205 excluded. An example: if you have two energy groups <tt>Protein</tt>
1206 and <tt>SOL</tt>, specifying
1208 <tt>energygrp-excl = Protein Protein SOL SOL</tt>
1210 would give only the non-bonded interactions between the protein and the
1211 solvent. This is especially useful for speeding up energy calculations with
1212 <tt>mdrun -rerun</tt> and for excluding interactions within frozen groups.</dd>
1215 <A NAME="walls"><br>
1217 <h3>Walls<!--QuietIdx-->walls<!--EQuietIdx--></h3>
1219 <dt><b>nwall: 0</b></dt>
1220 <dd>When set to <b>1</b> there is a wall at <tt>z=0</tt>, when set to <b>2</b>
1221 there is also a wall at <tt>z=z-box</tt>. Walls can only be used with <b>pbc=xy</b>.
1222 When set to <b>2</b> pressure coupling and Ewald summation can be used
1223 (it is usually best to use semiisotropic pressure coupling with
1224 the <tt>x/y</tt> compressibility set to 0, as otherwise the surface area will change).
1225 Walls interact wit the rest of the system through an optional <tt>wall-atomtype</tt>.
1226 Energy groups <tt>wall0</tt> and <tt>wall1</tt> (for <b>nwall=2</b>) are
1227 added automatically to monitor the interaction of energy groups
1229 The <A HREF="#run">center of mass motion removal</A> will be turned
1230 off in the <tt>z</tt>-direction.</dd>
1231 <dt><b>wall-atomtype:</b></dt>
1232 <dd>the atom type name in the force field for each wall.
1233 By (for example) defining a special wall atom type in the topology with its
1234 own combination rules, this allows for independent tuning of the interaction
1235 of each atomtype with the walls.</dd>
1236 <dt><b>wall-type:</b></dt>
1239 <dd>LJ integrated over the volume behind the wall: 9-3 potential</dd>
1240 <dt><b>10-4</b></dt>
1241 <dd>LJ integrated over the wall surface: 10-4 potential</dd>
1242 <dt><b>12-6</b></dt>
1243 <dd>direct LJ potential with the z distance from the wall</dd>
1244 <dt><b>table</b></dt><dd>user defined potentials indexed with the z distance from the wall, the tables are read analogously to
1245 the <b><A HREF="#table">energygrp-table</A></b> option,
1246 where the first name is for a ``normal'' energy group and the second name
1247 is <tt>wall0</tt> or <tt>wall1</tt>,
1248 only the dispersion and repulsion columns are used</dd>
1250 <dt><b>wall-r-linpot: -1 (nm)</b></dt>
1251 <dd>Below this distance from the wall the potential is continued
1252 linearly and thus the force is constant. Setting this option to
1253 a postive value is especially useful for equilibration when some atoms
1255 When the value is ≤0 (<0 for <b>wall-type=table</b>),
1256 a fatal error is generated when atoms are beyond a wall.
1258 <dt><b>wall-density: [nm<sup>-3</sup>/nm<sup>-2</sup>]</b></dt>
1259 <dd>the number density of the atoms for each wall for wall types
1260 <b>9-3</b> and <b>10-4</b>
1261 <dt><b>wall-ewald-zfac: 3</b></dt>
1262 <dd>The scaling factor for the third box vector for Ewald summation only,
1264 Ewald summation can only be used with <b>nwall=2</b>, where one
1265 should use <b><A HREF="#ewald">ewald-geometry</A><tt>=3dc</tt></b>.
1266 The empty layer in the box serves to decrease the unphysical Coulomb
1267 interaction between periodic images.
1272 <h3>COM <!--Idx-->pulling<!--EIdx--></h3>
1274 <dt><b>pull:</b></dt>
1277 <dd>No center of mass pulling.
1278 All the following pull options will be ignored
1279 (and if present in the <tt>.mdp</tt> file, they unfortunately generate warnings)</dd>
1280 <dt><b>umbrella</b></dt>
1281 <dd>Center of mass pulling using an umbrella potential
1282 between the reference group and one or more groups.</dd>
1283 <dt><b>constraint</b></dt>
1284 <dd>Center of mass pulling using a constraint
1285 between the reference group and one or more groups.
1286 The setup is identical to the option <b>umbrella</b>, except for the fact
1287 that a rigid constraint is applied instead of a harmonic potential.</dd>
1288 <dt><b>constant-force</b></dt>
1289 <dd>Center of mass pulling using a linear potential and therefore
1290 a constant force. For this option there is no reference position
1291 and therefore the parameters <b>pull-init</b> and <b>pull-rate</b>
1294 <dt><b>pull-geometry:</b></dt>
1296 <dt><b>distance</b></dt>
1297 <dd>Pull along the vector connecting the two groups.
1298 Components can be selected with <b>pull-dim</b>.</dd>
1299 <dt><b>direction</b></dt>
1300 <dd>Pull in the direction of <b>pull-vec</b>.</dd>
1301 <dt><b>direction-periodic</b></dt>
1302 <dd>As <b>direction</b>, but allows the distance to be larger than
1303 half the box size. With this geometry the box should not be dynamic
1304 (e.g. no pressure scaling) in the pull dimensions and the pull force
1305 is not added to virial.</dd>
1306 <dt><b>cylinder</b></dt>
1307 <dd>Designed for pulling with respect to a layer where the reference COM
1308 is given by a local cylindrical part of the reference group.
1309 The pulling is in the direction of <b>pull-vec</b>.
1310 From the reference group a cylinder is selected around the axis going
1311 through the pull group with direction <b>pull-vec</b> using two radii.
1312 The radius <b>pull-r1</b> gives the radius within which all
1313 the relative weights are one, between <b>pull-r1</b> and
1314 <b>pull-r0</b> the weights are switched to zero. Mass weighting is also used.
1315 Note that the radii should be smaller than half the box size.
1316 For tilted cylinders they should be even smaller than half the box size
1317 since the distance of an atom in the reference group
1318 from the COM of the pull group has both a radial and an axial component.
1319 <dt><b>position</b></dt>
1320 <dd>Pull to the position of the reference group plus
1321 <b>pull-init</b> + time*<b>pull-rate</b>*<b>pull-vec</b>.</dd>
1323 <dt><b>pull-dim: (Y Y Y)</b></dt>
1324 <dd>the distance components to be used with geometry <b>distance</b>
1325 and <b>position</b>, and also sets which components are printed
1326 to the output files</dd>
1327 <dt><b>pull-r1: (1) [nm]</b></dt>
1328 <dd>the inner radius of the cylinder for geometry <b>cylinder</b></dd>
1329 <dt><b>pull-r0: (1) [nm]</b></dt>
1330 <dd>the outer radius of the cylinder for geometry <b>cylinder</b></dd>
1331 <dt><b>pull-constr-tol: (1e-6)</b></dt>
1332 <dd>the relative constraint tolerance for constraint pulling</dd>
1333 <dt><b>pull-start:</b></dt>
1336 <dd>do not modify <b>pull-init</b>
1338 <dd>add the COM distance of the starting conformation to <b>pull-init</b></dd>
1340 <dt><b>pull-nstxout: (10)</b></dt>
1341 <dd>frequency for writing out the COMs of all the pull group</dd>
1342 <dt><b>pull-nstfout: (1)</b></dt>
1343 <dd>frequency for writing out the force of all the pulled group</dd>
1344 <dt><b>pull-ngroups: (1)</b></dt>
1345 <dd>The number of pull groups, not including the reference group.
1346 If there is only one group, there is no difference in treatment
1347 of the reference and pulled group (except with the cylinder geometry).
1348 Below only the pull options for the reference group (ending on 0)
1349 and the first group (ending on 1) are given,
1350 further groups work analogously, but with the number 1 replaced
1351 by the group number.</dd>
1352 <dt><b>pull-group0: </b></dt>
1353 <dd>The name of the reference group. When this is empty an absolute reference
1354 of (0,0,0) is used. With an absolute reference the system is no longer
1355 translation invariant and one should think about what to do with
1356 the <A HREF="#run">center of mass motion</A>.</dd>
1357 <dt><b>pull-weights0: </b></dt>
1358 <dd>see <b>pull-weights1</b></dd>
1359 <dt><b>pull-pbcatom0: (0)</b></dt>
1360 <dd>see <b>pull-pbcatom1</b></dd>
1361 <dt><b>pull-group1: </b></dt>
1362 <dd>The name of the pull group.</dd>
1363 <dt><b>pull-weights1: </b></dt>
1364 <dd>Optional relative weights which are multiplied with the masses of the atoms
1365 to give the total weight for the COM. The number should be 0, meaning all 1,
1366 or the number of atoms in the pull group.</dd>
1367 <dt><b>pull-pbcatom1: (0)</b></dt>
1368 <dd>The reference atom for the treatment of periodic boundary conditions
1370 (this has no effect on the treatment of the pbc between groups).
1371 This option is only important when the diameter of the pull group
1372 is larger than half the shortest box vector.
1373 For determining the COM, all atoms in the group are put at their periodic image
1374 which is closest to <b>pull-pbcatom1</b>.
1375 A value of 0 means that the middle atom (number wise) is used.
1376 This parameter is not used with geometry <b>cylinder</b>.
1377 A value of -1 turns on cosine weighting, which is useful for a group
1378 of molecules in a periodic system, e.g. a water slab (see Engin et al.
1379 J. Chem. Phys. B 2010).</dd>
1380 <dt><b>pull-vec1: (0.0 0.0 0.0)</b></dt>
1381 <dd>The pull direction. <tt>grompp</tt> normalizes the vector.</dd>
1382 <dt><b>pull-init1: (0.0) / (0.0 0.0 0.0) [nm]</b></dt>
1383 <dd>The reference distance at t=0. This is a single value,
1384 except for geometry <b>position</b> which uses a vector.</dd>
1385 <dt><b>pull-rate1: (0) [nm/ps]</b></dt>
1386 <dd>The rate of change of the reference position.</dd>
1387 <dt><b>pull-k1: (0) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
1388 <dd>The force constant. For umbrella pulling this is the harmonic force
1389 constant in [kJ mol<sup>-1</sup> nm<sup>-2</sup>]. For constant force pulling
1390 this is the force constant of the linear potential, and thus minus (!)
1391 the constant force in [kJ mol<sup>-1</sup> nm<sup>-1</sup>].</dd>
1392 <dt><b>pull-kB1: (pull-k1) [kJ mol<sup>-1</sup> nm<sup>-2</sup>] / [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
1393 <dd>As <b>pull-k1</b>, but for state B. This is only used when
1394 <A HREF="#free"><b>free-energy</b></A> is turned on.
1395 The force constant is then (1 - lambda)*<b>pull-k1</b> + lambda*<b>pull-kB1</b>.
1400 <h3><!--Idx-->NMR refinement<!--EIdx--></h3>
1402 <dt><b>disre:</b></dt>
1405 <dd>ignore <!--Idx-->distance restraint<!--EIdx--> information in topology file</dd>
1406 <dt><b>simple</b></dt>
1407 <dd>simple (per-molecule) distance restraints.
1408 <dt><b>ensemble</b></dt>
1409 <dd>distance restraints over an ensemble of molecules in one
1410 simulation box. Normally, one would perform ensemble averaging over
1411 multiple subsystems, each in a separate box, using <tt>mdrun -multi</tt>;s
1412 upply <tt>topol0.tpr</tt>, <tt>topol1.tpr</tt>, ... with different
1413 coordinates and/or velocities.
1414 The environment variable <tt>GMX_DISRE_ENSEMBLE_SIZE</tt> sets the number
1415 of systems within each ensemble (usually equal to the <tt>mdrun -multi</tt> value).</dd>
1418 <dt><b>disre-weighting:</b></dt>
1420 <dt><b>equal</b> (default)</dt>
1421 <dd>divide the restraint force equally over all atom pairs in the restraint</dd>
1422 <dt><b>conservative</b></dt>
1423 <dd>the forces are the derivative of the restraint potential,
1424 this results in an r<sup>-7</sup> weighting of the atom pairs.
1425 The forces are conservative when <tt>disre-tau</tt> is zero.</dd>
1427 <dt><b>disre-mixed:</b></dt>
1430 <dd>the violation used in the calculation of the restraint force is the
1431 time-averaged violation </dd>
1433 <dd>the violation used in the calculation of the restraint force is the
1434 square root of the product of the time-averaged violation and the instantaneous violation</dd>
1437 <dt><b>disre-fc: (1000) [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
1438 <dd>force constant for distance restraints, which is multiplied by a
1439 (possibly) different factor for each restraint given in the <tt>fac</tt>
1440 column of the interaction in the topology file.</dd>
1442 <dt><b>disre-tau: (0) [ps]</b></dt>
1443 <dd>time constant for distance restraints running average. A value of zero turns off time averaging.</dd>
1445 <dt><b>nstdisreout: (100) [steps]</b></dt>
1446 <dd>period between steps when the running time-averaged and instantaneous distances
1447 of all atom pairs involved in restraints are written to the energy file
1448 (can make the energy file very large)</dd>
1451 <dt><b>orire:</b></dt>
1454 <dd>ignore <!--Idx-->orientation restraint<!--EIdx--> information in topology file</dd>
1456 <dd>use orientation restraints, ensemble averaging can be performed
1457 with <tt>mdrun -multi</tt></dd>
1459 <dt><b>orire-fc: (0) [kJ mol]</b></dt>
1460 <dd>force constant for orientation restraints, which is multiplied by a
1461 (possibly) different weight factor for each restraint, can be set to zero to
1462 obtain the orientations from a free simulation</dd>
1463 <dt><b>orire-tau: (0) [ps]</b></dt>
1464 <dd>time constant for orientation restraints running average. A value of zero turns off time averaging.</dd>
1465 <dt><b>orire-fitgrp: </b></dt>
1466 <dd>fit group for orientation restraining. This group of atoms is used
1467 to determine the rotation <b>R</b> of the system with respect to the
1468 reference orientation. The reference orientation is the starting
1469 conformation of the first subsystem. For a protein, backbone is a reasonable
1471 <dt><b>nstorireout: (100) [steps]</b></dt>
1472 <dd>period between steps when the running time-averaged and instantaneous orientations
1473 for all restraints, and the molecular order tensor are written to the energy file
1474 (can make the energy file very large)</dd>
1479 <h3>Free energy calculations<!--QuietIdx-->free energy calculations<!--EQuietIdx--></h3>
1482 <dt><b>free-energy:</b></dt>
1485 <dd>Only use topology A.</dd>
1487 <dd>Interpolate between topology A (lambda=0) to topology B (lambda=1)
1488 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
1489 the energy file and/or to <tt>dhdl.xvg</tt>, where they can be processed by, for example <tt>g_bar</tt>.
1490 The potentials, bond-lengths and angles are interpolated linearly as
1491 described in the manual. When <b>sc-alpha</b> is larger than zero, soft-core
1492 potentials are used for the LJ and Coulomb interactions.</dd>
1493 <dt><b>expanded</b></dt>
1494 <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>
1496 <dt><b>init-lambda: (-1)</b></dt>
1497 <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>
1498 <dt><b>delta-lambda: (0)</b></dt>
1499 <dd>increment per time step for lambda</dd>
1500 <dt><b>init-lambda-state: (-1)</b></dt>
1501 <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>
1502 <dt><b>fep-lambdas: ()</b></dt>
1503 <dd>Zero, one or more lambda values for which Delta H values will
1504 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps.
1505 Values must be between 0 and 1.
1506 Free energy differences between different lambda values can then
1507 be determined with <tt>g_bar</tt>. <b>fep-lambdas</b> is different from the other -lambdas keywords because
1508 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>
1509 <dt><b>coul-lambdas: ()</b></dt>
1510 <dd>Zero, one or more lambda values for which Delta H values will
1511 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1512 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>
1513 <dt><b>vdw-lambdas: ()</b></dt>
1514 <dd>Zero, one or more lambda values for which Delta H values will
1515 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1516 Only the van der Waals interactions are controlled with this component of the lambda vector.</dd>
1517 <dt><b>bonded-lambdas: ()</b></dt>
1518 <dd>Zero, one or more lambda values for which Delta H values will
1519 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1520 Only the bonded interactions are controlled with this component of the lambda vector.</dd>
1521 <dt><b>restraint-lambdas: ()</b></dt>
1522 <dd>Zero, one or more lambda values for which Delta H values will
1523 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1524 Only the restraint interactions: dihedral restraints, and the pull code restraints are controlled with this component of the lambda vector. </dd>
1525 <dt><b>mass-lambdas: ()</b></dt>
1526 <dd>Zero, one or more lambda values for which Delta H values will
1527 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1528 Only the particle masses are controlled with this component of the lambda vector.</dd>
1529 <dt><b>temperature-lambdas: ()</b></dt>
1530 <dd>Zero, one or more lambda values for which Delta H values will
1531 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps. Values must be between 0 and 1.
1532 Only the temperatures controlled with this component of the lambda vector.
1533 Note that these lambdas should not be used for replica exchange, only for simulated tempering.</dd>
1534 <dt><b>calc-lambda-neighbors (1)</b></dt>
1535 <dd>Controls the number of lambda values for which Delta H values will be
1536 calculated and written out, if <b>init-lambda-state</b> has been set. A
1537 positive value will limit the number of lambda points calculated to only the
1538 nth neighbors of <b>init-lambda-state</b>: for example, if
1539 <b>init-lambda-state</b> is 5 and this parameter has a value of 2, energies for
1540 lambda points 3-7 will be calculated and writen out. A value of -1 means all
1541 lambda points will be written out. For normal BAR such as with g_bar, a value
1542 of 1 is sufficient, while for MBAR -1 should be used.</dd>
1543 <dt><b>sc-alpha: (0)</b></dt>
1544 <dd>the soft-core alpha parameter, a value of 0 results in linear interpolation of the LJ and Coulomb interactions</dd>
1545 <dt><b>sc-r-power: (6)</b></dt>
1546 <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>
1547 <dt><b>sc-coul: (no)</b></dt>
1548 <dd>Whether to apply the soft core free energy interations to the Columbic interaction. Default is no, as it is generally
1549 more efficient to turn of the Coulomic interactions linearly before turning off electrostatic interactions.</dd>
1550 <dt><b>sc-power: (0)</b></dt>
1551 <dd>the power for lambda in the soft-core function, only the values 1 and 2 are supported</dd>
1552 <dt><b>sc-sigma: (0.3) [nm]</b></dt>
1553 <dd>the soft-core sigma for particles which have a C6 or C12 parameter equal
1554 to zero or a sigma smaller than <b>sc-sigma</b></dd>
1555 <dt><b>couple-moltype:</b></dt>
1556 <dd>Here one can supply a molecule type (as defined in the topology)
1557 for calculating solvation or coupling free energies.
1558 There is a special option <b>system</b> that couples all molecule types
1559 in the system. This can be useful for equilibrating a system
1560 starting from (nearly) random coordinates.
1561 <b>free-energy</b> has to be turned on.
1562 The Van der Waals interactions and/or charges in this molecule type can be
1563 turned on or off between lambda=0 and lambda=1, depending on the settings
1564 of <b>couple-lambda0</b> and <b>couple-lambda1</b>. If you want to decouple
1565 one of several copies of a molecule, you need to copy and rename
1566 the molecule definition in the topology.</dd>
1567 <dt><b>couple-lambda0:</b></dt>
1569 <dt><b>vdw-q</b></dt>
1570 <dd>all interactions are on at lambda=0
1572 <dd>the charges are zero (no Coulomb interactions) at lambda=0
1574 <dd>the Van der Waals interactions are turned at lambda=0; soft-core interactions will be required to avoid singularities
1575 <dt><b>none</b></dt>
1576 <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.
1578 <dt><b>couple-lambda1:</b></dt>
1579 <dd> analogous to <b>couple-lambda1</b>, but for lambda=1
1580 <dt><b>couple-intramol:</b></dt>
1583 <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.
1585 <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.
1587 <dt><b>nstdhdl: (100)</b></dt>
1588 <dd>the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg,
1589 0 means no ouput, should be a multiple of <b>nstcalcenergy</b></dd>.</dd>
1590 <dt><b>dhdl-derivatives: (yes)</b></dt>
1591 <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>
1592 <dt><b>dhdl-print-energy: (no)</b></dt>
1593 <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>
1594 <dt><b>separate-dhdl-file: (yes)</b></dt>
1597 <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>
1599 <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>
1601 <dt><b>dh-hist-size: (0)</b></dt>
1602 <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>
1603 <dt><b>dh-hist-spacing (0.1)</b></dt>
1604 <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>
1606 <A NAME="expanded"><br>
1608 <h3><!--Idx-->Expanded Ensemble calculations<!--EIdx--></h3>
1611 <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>
1612 <dt><b>lmc-stats:</b></dt>
1615 <dd>No Monte Carlo in state space is performed.</dd>
1616 <dt><b>metropolis-transition</b></dt>
1617 <dd> Uses the Metropolis weights to update the expanded ensemble weight of each state.
1618 Min{1,exp(-(beta_new u_new - beta_old u_old)}</dd>
1619 <dt><b>barker-transition</b></dt>
1620 <dd> Uses the Barker transition critera to update the expanded ensemble weight of each state i, defined by
1621 exp(-beta_new u_new)/[exp(-beta_new u_new)+exp(-beta_old u_old)</dd>
1622 <dt><b>wang-landau</b></dt>
1623 <dd>Uses the Wang-Landau algorithm (in state space, not energy space) to update the expanded ensemble weights.</dd>
1624 <dt><b>min-variance</b></dt>
1625 <dd>Uses the minimum variance updating method of Escobedo et al. to update the expanded ensemble weights. Weights
1626 will not be the free energies, but will rather emphasize states that need more sampling to give even uncertainty.</dd>
1628 <dt><b>lmc-mc-move:</b></dt>
1631 <dd>No Monte Carlo in state space is performed.</dd>
1632 <dt><b>metropolis-transition</b></dt>
1633 <dd> Randomly chooses a new state up or down, then uses the Metropolis critera to decide whether to accept or reject:
1634 Min{1,exp(-(beta_new u_new - beta_old u_old)}</dd>
1635 <dt><b>barker-transition</b></dt>
1636 <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>
1637 <dt><b>gibbs</b></dt>
1638 <dd> Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to
1639 decide which state to move to.</dd>
1640 <dt><b>metropolized-gibbs</b></dt>
1642 <dd> Uses the conditional weights of the state given the coordinate (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to
1643 decide which state to move to, EXCLUDING the current state, then uses a rejection step to ensure detailed
1644 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>
1646 <dt><b>lmc-seed:</b></dt>
1647 <dd> random seed to use for Monte Carlo moves in state space. If not specified, <b>ld-seed</b> is used instead.</dd>
1648 <dt><b>mc-temperature:</b></dt>
1649 <dd> Temperature used for acceptance/rejection for Monte Carlo moves. If not specified, the temperature of the
1650 simulation specified in the first group of <b>ref_t</b> is used.</dd>
1651 <dt><b>wl-ratio: (0.8)</b></dt>
1652 <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>
1653 <dt><b>wl-scale: (0.8)</b></dt>
1654 <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>
1655 <dt><b>init-wl-delta: (1.0)</b></dt>
1656 <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>
1657 <dt><b>wl-oneovert: (no)</b></dt>
1658 <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>
1659 <dt><b>lmc-repeats: (1)</b></dt>
1660 <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>
1661 <dt><b>lmc-gibbsdelta: (-1)</b></dt>
1662 <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>
1663 <dt><b>lmc-forced-nstart: (0)</b></dt>
1664 <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.
1665 <dt><b>nst-transition-matrix: (-1)</b></dt>
1666 <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>
1667 <dt><b>symmetrized-transition-matrix: (no) </b></dt>
1668 <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>
1669 <dt><b>mininum-var-min: (100)</b></dt>
1670 <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>
1671 <dt><b>init-lambda-weights: </b></dt>
1672 <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>
1673 <dt><b>lmc-weights-equil: (no)</b></dt>
1676 <dd>Expanded ensemble weights continue to be updated throughout the simulation.</dd>
1678 <dd>The input expanded ensemble weights are treated as equilibrated, and are not updated throughout the simulation.</dd>
1679 <dt><b>wl-delta</b></dt>
1680 <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>
1681 <dt><b>number-all-lambda</b></dt>
1682 <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>
1683 <dt><b>number-steps</b></dt>
1684 <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>
1685 <dt><b>number-samples</b></dt>
1686 <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>
1687 <dt><b>count-ratio</b></dt>
1688 <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>
1690 <dt><b>simulated-tempering: (no)</b></dt>
1691 <dd>Turn simulated tempering on or off. Simulated tempering is implemented as expanded ensemble sampling with different temperatures instead of different Hamiltonians.</dd>
1692 <dt><b>sim-temp-low: (300)</b></dt>
1693 <dd>Low temperature for simulated tempering.</dd>
1694 <dt><b>sim-temp-high: (300)</b></dt>
1695 <dd>High temperature for simulated tempering.</dd>
1696 <dt><b>simulated-tempering-scaling: (linear)</b></dt>
1697 <dd>Controls the way that the temperatures at intermediate lambdas are calculated from the <b>temperature-lambda</b> part of the lambda vector.</dd>
1699 <dt><b>linear</b></dt>
1700 <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>
1701 <dt><b>geometric</b></dt>
1702 <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>
1703 <dt><b>exponential</b></dt>
1704 <dd> Interpolates temperatures exponentially between <b>sim-temp-low</b> and <b>sim-temp-high</b>. The ith state has temperature
1705 <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>
1711 <h3>Non-equilibrium MD<!--QuietIdx-->non-equilibrium MD<!--EQuietIdx--></h3>
1714 <dt><b>acc-grps: </b></dt>
1715 <dd>groups for constant acceleration (e.g.: <tt>Protein Sol</tt>)
1716 all atoms in groups Protein and Sol will experience constant acceleration
1717 as specified in the <b>accelerate</b> line</dd>
1718 <dt><b>accelerate: (0) [nm ps<sup>-2</sup>]</b></dt>
1719 <dd>acceleration for <b>acc-grps</b>; x, y and z for each group
1720 (e.g. <tt>0.1 0.0 0.0 -0.1 0.0 0.0</tt> means that first group has constant
1721 acceleration of 0.1 nm ps<sup>-2</sup> in X direction, second group the
1723 <dt><b>freezegrps: </b></dt>
1724 <dd>Groups that are to be frozen (i.e. their X, Y, and/or Z position will
1725 not be updated; e.g. <tt>Lipid SOL</tt>). <b>freezedim</b> specifies for
1726 which dimension the freezing applies.
1727 To avoid spurious contibrutions to the virial and pressure due to large
1728 forces between completely frozen atoms you need to use
1729 <A HREF="#egexcl">energy group exclusions</A>, this also saves computing time.
1730 Note that coordinates of frozen atoms are not scaled by pressure-coupling
1732 <dt><b>freezedim: </b></dt>
1733 <dd>dimensions for which groups in <b>freezegrps</b> should be frozen,
1734 specify <tt>Y</tt> or <tt>N</tt> for X, Y and Z and for each group
1735 (e.g. <tt>Y Y N N N N</tt> means that particles in the first group
1736 can move only in Z direction. The particles in the second group can
1737 move in any direction).</dd>
1738 <dt><b>cos-acceleration: (0) [nm ps<sup>-2</sup>]</b></dt>
1739 <dd>the amplitude of the acceleration profile for calculating the
1740 <!--Idx-->viscosity<!--EIdx-->.
1741 The acceleration is in the X-direction and the magnitude is
1742 <b>cos-acceleration</b> cos(2 pi z/boxheight).
1743 Two terms are added to the energy file:
1744 the amplitude of the velocity profile and 1/viscosity.</dd>
1745 <dt><b><!--Idx-->deform<!--EIdx-->: (0 0 0 0 0 0) [nm ps<sup>-1</sup>]</b></dt>
1746 <dd>The velocities of deformation for the box elements:
1747 a(x) b(y) c(z) b(x) c(x) c(y). Each step the box elements
1748 for which <b>deform</b> is non-zero are calculated as:
1749 box(ts)+(t-ts)*deform, off-diagonal elements are corrected
1750 for periodicity. The coordinates are transformed accordingly.
1751 Frozen degrees of freedom are (purposely) also transformed.
1752 The time ts is set to t at the first step and at steps at which
1753 x and v are written to trajectory to ensure exact restarts.
1754 Deformation can be used together with semiisotropic or anisotropic
1755 pressure coupling when the appropriate compressibilities are set to zero.
1756 The diagonal elements can be used to <!--Idx-->strain<!--EIdx--> a solid.
1757 The off-diagonal elements can be used to <!--Idx-->shear<!--EIdx--> a solid
1763 <h3>Electric fields<!--QuietIdx-->electric field<!--EQuietIdx--></h3>
1766 <dt><b>E-x ; E-y ; E-z:</b></dt>
1767 <dd>If you want to use an electric field in a direction, enter 3 numbers
1768 after the appropriate <b>E-*</b>, the first number: the number of cosines,
1769 only 1 is implemented (with frequency 0) so enter 1,
1770 the second number: the strength of the electric field in
1771 <b>V nm<sup>-1</sup></b>,
1772 the third number: the phase of the cosine, you can enter any number here
1773 since a cosine of frequency zero has no phase.</dd>
1774 <dt><b>E-xt; E-yt; E-zt: </b></dt>
1775 <dd>not implemented yet</dd>
1781 <h3>Mixed quantum/classical molecular dynamics<!--QuietIdx>QM/MM<!--EQuietIdx--></h3>
1784 <dt><b>QMMM:</b></dt>
1785 <dd><dl compact="compact">
1789 <dd>Do a QM/MM simulation. Several groups can be described at
1790 different QM levels separately. These are specified in
1791 the <b>QMMM-grps</b> field separated by spaces. The level of <i>ab
1792 initio</i> theory at which the groups are described is specified
1793 by <b>QMmethod</b> and <b>QMbasis</b> Fields. Describing the
1794 groups at different levels of theory is only possible with the ONIOM
1795 QM/MM scheme, specified by <b>QMMMscheme</b>.</dd>
1798 <dt><b>QMMM-grps:</b></dt>
1799 <dd>groups to be descibed at the QM level</dd>
1801 <dt><b>QMMMscheme:</b></dt>
1802 <dd><dl compact="compact">
1803 <dt><b>normal</b></dt>
1804 <dd>normal QM/MM. There can only be one <b>QMMM-grps</b> that is modelled
1805 at the <b>QMmethod</b> and <b>QMbasis</b> level of <i>ab initio</i>
1806 theory. The rest of the system is described at the MM level. The QM
1807 and MM subsystems interact as follows: MM point charges are included
1808 in the QM one-electron hamiltonian and all Lennard-Jones interactions
1809 are described at the MM level.</dd>
1810 <dt><b>ONIOM</b></dt>
1811 <dd>The interaction between the subsystem is described using the ONIOM
1812 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
1813 (<b>QMmethod</b> and <b>QMbasis</b>).
1816 <dt><b>QMmethod: (RHF)</b></dt>
1817 <dd>Method used to compute the energy and gradients on the QM
1818 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
1819 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
1820 included in the active space is specified by <b>CASelectrons</b>
1821 and <b>CASorbitals</b>. </dd>
1823 <dt><b>QMbasis: (STO-3G)</b></dt>
1824 <dd>Basis set used to expand the electronic wavefuntion. Only Gaussian
1825 basis sets are currently available, <i>i.e.</i> STO-3G, 3-21G, 3-21G*,
1826 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*, and 6-311G.</dd>
1828 <dt><b>QMcharge: (0) [integer]</b></dt>
1829 <dd>The total charge in <tt>e</tt> of the <b>QMMM-grps</b>. In case
1830 there are more than one <b>QMMM-grps</b>, the total charge of each
1831 ONIOM layer needs to be specified separately.</dd>
1833 <dt><b>QMmult: (1) [integer]</b></dt>
1834 <dd>The multiplicity of the <b>QMMM-grps</b>. In case there are more
1835 than one <b>QMMM-grps</b>, the multiplicity of each ONIOM layer needs
1836 to be specified separately.</dd>
1838 <dt><b>CASorbitals: (0) [integer]</b></dt>
1839 <dd>The number of orbitals to be included in the active space when
1840 doing a CASSCF computation.</dd>
1842 <dt><b>CASelectrons: (0) [integer]</b></dt>
1843 <dd>The number of electrons to be included in the active space when
1844 doing a CASSCF computation.</dd>
1847 <dd><dl compact="compact">
1849 <dd>No surface hopping. The system is always in the electronic
1852 <dd>Do a QM/MM MD simulation on the excited state-potential energy
1853 surface and enforce a <i>diabatic</i> hop to the ground-state when the
1854 system hits the conical intersection hyperline in the course the
1855 simulation. This option only works in combination with the CASSCF
1862 <h3>Implicit solvent</h3>
1865 <dt><b>implicit-solvent:</b></dt>
1866 <dd><dl compact="compact">
1868 <dd>No implicit solvent</dd>
1869 <dt><b>GBSA</b></dt>
1870 <dd>Do a simulation with implicit solvent using the Generalized Born formalism.
1871 Three different methods for calculating the Born radii are available, Still, HCT and
1872 OBC. These are specified with the <b>gb-algorithm</b> field. The non-polar solvation
1873 is specified with the <b>sa-algorithm</b> field.</dd>
1876 <dt><b>gb-algorithm:</b></dt>
1877 <dd><dl compact="compact">
1878 <dt><b>Still</b></dt>
1879 <dd>Use the Still method to calculate the Born radii</dd>
1881 <dd>Use the Hawkins-Cramer-Truhlar method to calculate the Born radii</dd>
1883 <dd>Use the Onufriev-Bashford-Case method to calculate the Born radii</dd>
1886 <dt><b>nstgbradii: (1) [steps]</b></dt>
1887 <dd>Frequency to (re)-calculate the Born radii. For most practial purposes,
1888 setting a value larger than 1 violates energy conservation and leads to
1889 unstable trajectories.</dd>
1891 <dt><b>rgbradii: (1.0) [nm]</b></dt>
1892 <dd>Cut-off for the calculation of the Born radii. Currently must be equal to rlist</dd>
1894 <dt><b>gb-epsilon-solvent: (80)</b></dt>
1895 <dd>Dielectric constant for the implicit solvent</dd>
1897 <dt><b>gb-saltconc: (0) [M]</b></dt>
1898 <dd>Salt concentration for implicit solvent models, currently not used</dd>
1900 <dt><b>gb-obc-alpha (1); gb-obc-beta (0.8); gb-obc-gamma (4.85);</b></dt>
1901 <dd>Scale factors for the OBC model. Default values are OBC(II).
1902 Values for OBC(I) are 0.8, 0 and 2.91 respectively</dd>
1904 <dt><b>gb-dielectric-offset: (0.009) [nm]</b></dt>
1905 <dd>Distance for the di-electric offset when calculating the Born radii. This is
1906 the offset between the center of each atom the center of the polarization energy
1907 for the corresponding atom</dd>
1909 <dt><b>sa-algorithm</b></dt>
1910 <dd><dl compact="compact">
1911 <dt><b>Ace-approximation</b></dt>
1912 <dd>Use an Ace-type approximation (default)</dd>
1913 <dt><b>None</b></dt>
1914 <dd>No non-polar solvation calculation done. For GBSA only the polar part gets
1918 <dt><b>sa-surface-tension: [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
1919 <dd>Default value for surface tension with SA algorithms. The default value is -1;
1920 Note that if this default value is not changed
1921 it will be overridden by <tt>grompp</tt> using values that are specific for the choice
1922 of radii algorithm (0.0049 kcal/mol/Angstrom<sup>2</sup> for Still, 0.0054 kcal/mol/Angstrom<sup>2</sup>
1925 Setting it to 0 will while using an sa-algorithm other than None means
1926 no non-polar calculations are done.
1930 <A NAME="adress"><br>
1932 <h3>Adaptive Resolution Simulation</h3>
1935 <dt><b>adress: (no)</b></dt>
1936 <dd>Decide whether the AdResS feature is turned on.</dd>
1937 <dt><b>adress-type: (Off)</b></dt>
1940 <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>
1941 <dt><b>Constant</b></dt>
1942 <dd>Do an AdResS simulation with a constant weight, <b>adress-const-wf</b> defines the value of the weight</dd>
1943 <dt><b>XSplit</b></dt>
1944 <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>
1945 <dt><b>Sphere</b></dt>
1946 <dd>Do an AdResS simulation with spherical explicit zone.</dd>
1948 <dt><b>adress-const-wf: (1)</b></dt>
1949 <dd>Provides the weight for a constant weight simulation (<b>adress-type</b>=Constant)</dd>
1950 <dt><b>adress-ex-width: (0)</b></dt>
1951 <dd>Width of the explicit zone, measured from <b>adress-reference-coords</b>.</dd>
1952 <dt><b>adress-hy-width: (0)</b></dt>
1953 <dd>Width of the hybrid zone.</dd>
1954 <dt><b>adress-reference-coords: (0,0,0)</b></dt>
1955 <dd>Position of the center of the explicit zone. Periodic boundary conditions apply for measuring the distance from it.</dd>
1956 <dt><b>adress-cg-grp-names</b></dt>
1957 <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>
1958 <dt><b>adress-site: (COM)</b>The mapping point from which the weight is calculated.</dt>
1961 <dd>The weight is calculated from the center of mass of each charge group.</dd>
1963 <dd>The weight is calculated from the center of geometry of each charge group.</dd>
1964 <dt><b>Atom</b></dt>
1965 <dd>The weight is calculated from the position of 1st atom of each charge group.</dd>
1966 <dt><b>AtomPerAtom</b></dt>
1967 <dd>The weight is calculated from the position of each individual atom.</dd>
1969 <dt><b>adress-interface-correction: (Off)</b></dt>
1972 <dd>Do not a apply any interface correction.</dd>
1973 <dt><b>thermoforce</b></dt>
1974 <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>
1976 <dt><b>adress-tf-grp-names</b></dt>
1977 <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>
1978 <dt><b>adress-ex-forcecap: (0)</b></dt>
1979 <dd>Cap the force in the hybrid region, useful for big molecules. 0 disables force capping.</dd>
1984 <h3>User defined thingies</h3>
1987 <dt><b>user1-grps; user2-grps: </b></dt>
1988 <dt><b>userint1 (0); userint2 (0); userint3 (0); userint4 (0)</b></dt>
1989 <dt><b>userreal1 (0); userreal2 (0); userreal3 (0); userreal4 (0)</b></dt>
1990 <dd>These you can use if you modify code. You can pass integers and
1991 reals to your subroutine. Check the inputrec definition in
1992 <tt>src/include/types/inputrec.h</tt></dd>
2003 <A HREF="#neq">acc-grps</A><br>
2004 <A HREF="#neq">accelerate</A><br>
2005 <A HREF="#sa">annealing</A><br>
2006 <A HREF="#sa">annealing-npoints</A><br>
2007 <A HREF="#sa">annealing-time</A><br>
2008 <A HREF="#sa">annealing-temp</A><br>
2009 <A HREF="#ld">bd-fric</A><br>
2010 <A HREF="#vdw">bDispCorr</A><br>
2011 <A HREF="#run">comm-mode</A><br>
2012 <A HREF="#run">comm-grps</A><br>
2013 <A HREF="#pc">compressibility</A><br>
2014 <A HREF="#bond">constraint-algorithm</A><br>
2015 <A HREF="#bond">constraints</A><br>
2016 <A HREF="#neq">cos-acceleration</A><br>
2017 <A HREF="#el">coulombtype</A><br>
2018 <A HREF="#el">coulomb-modifier</A><br>
2019 <A HREF="#free">couple-intramol</A><br>
2020 <A HREF="#free">couple-lambda0</A><br>
2021 <A HREF="#free">couple-lambda1</A><br>
2022 <A HREF="#free">couple-moltype</A><br>
2023 <A HREF="#nl">cutoff-scheme</A><br>
2024 <A HREF="#pp">define</A><br>
2025 <A HREF="#neq">deform</A><br>
2026 <A HREF="#free">delta-lambda</A><br>
2027 <A HREF="#nmr">disre</A><br>
2028 <A HREF="#nmr">disre-weighting</A><br>
2029 <A HREF="#nmr">disre-mixed</A><br>
2030 <A HREF="#nmr">disre-fc</A><br>
2031 <A HREF="#nmr">disre-tau</A><br>
2032 <A HREF="#run">dt</A><br>
2033 <A HREF="#em">emstep</A><br>
2034 <A HREF="#em">emtol</A><br>
2035 <A HREF="#egexcl">energygrp-excl</A><br>
2036 <A HREF="#table">energygrp-table</A><br>
2037 <A HREF="#out">energygrps</A><br>
2038 <A HREF="#el2">epsilon-r</A><br>
2039 <A HREF="#el2">epsilon-rf</A><br>
2040 <A HREF="#ewald">ewald-rtol</A><br>
2041 <A HREF="#ewald">ewald-geometry</A><br>
2042 <A HREF="#ewald">epsilon-surface</A><br>
2043 <A HREF="#ef">E-x</A><br>
2044 <A HREF="#ef">E-xt</A><br>
2045 <A HREF="#ef">E-y</A><br>
2046 <A HREF="#ef">E-yt</A><br>
2047 <A HREF="#ef">E-z</A><br>
2048 <A HREF="#ef">E-zt </A><br>
2049 <A HREF="#xmdrun">fcstep</A><br>
2050 <A HREF="#ewald">fourier-nx</A><br>
2051 <A HREF="#ewald">fourier-ny</A><br>
2052 <A HREF="#ewald">fourier-nz</A><br>
2053 <A HREF="#ewald">fourierspacing</A><br>
2054 <A HREF="#free">free-energy</A><br>
2055 <A HREF="#neq">freezedim </A><br>
2056 <A HREF="#neq">freezegrps</A><br>
2057 <A HREF="#vel">gen-seed</A><br>
2058 <A HREF="#vel">gen-temp</A><br>
2059 <A HREF="#vel">gen-vel</A><br>
2060 <A HREF="#pp">include</A><br>
2061 <A HREF="#free">init-lambda</A><br>
2062 <A HREF="#expanded">init-lambda-weights</A><br>
2063 <A HREF="#run">init-step</A><br>
2064 <A HREF="#expanded">initial-wl-delta</A><br>
2065 <A HREF="#run">integrator</A><br>
2066 <A HREF="#ld">ld-seed</A><br>
2067 <A HREF="#bond2">lincs-iter</A><br>
2068 <A HREF="#bond2">lincs-order</A><br>
2069 <A HREF="#bond2">lincs-warnangle</A><br>
2070 <A HREF="#expanded">lmc-forced-nstart</A><br>
2071 <A HREF="#expanded">lmc-gibbsdelta</A><br>
2072 <A HREF="#expanded">lmc-mc-move</A><br>
2073 <A HREF="#expanded">lmc-seed</A><br>
2074 <A HREF="#expanded">lmc-stats</A><br>
2075 <A HREF="#expanded">lmc-weights-equil</A><br>
2076 <A HREF="#expanded">mc-temperature</A><br>
2077 <A HREF="#expanded">mininum-var-min</A><br>
2078 <A HREF="#bond2">morse</A><br>
2079 <A HREF="#em">nbfgscorr</A><br>
2080 <A HREF="#xmdrun">niter</A><br>
2081 <A HREF="#tc">nh-chain-length</A><br>
2082 <A HREF="#em">nstcgsteep</A><br>
2083 <A HREF="#out">nstcalcenergy</A><br>
2084 <A HREF="#run">nstcomm</A><br>
2085 <A HREF="#nmr">nstdisreout</A><br>
2086 <A HREF="#out">nstenergy</A><br>
2087 <A HREF="#run">nsteps</A><br>
2088 <A HREF="#out">nstfout</A><br>
2089 <A HREF="#nl">nstlist</A><br>
2090 <A HREF="#out">nstlog</A><br>
2091 <A HREF="#pc">nstpcouple</A><br>
2092 <A HREF="#tc">nsttcouple</A><br>
2093 <A HREF="#out">nstvout</A><br>
2094 <A HREF="#out">nstxout</A><br>
2095 <A HREF="#out">nstxtcout</A><br>
2096 <A HREF="#expanded">nst-transition-matrix</A><br>
2097 <A HREF="#nl">ns-type</A><br>
2098 <A HREF="#wall">nwall</A><br>
2099 <A HREF="#ewald">optimize-fft</A><br>
2100 <A HREF="#nmr2">orire</A><br>
2101 <A HREF="#nmr2">orire-fc</A><br>
2102 <A HREF="#nmr2">orire-tau</A><br>
2103 <A HREF="#nmr2">orire-fitgrp</A><br>
2104 <A HREF="#nmr2">nstorireout</A><br>
2105 <A HREF="#nl">pbc</A><br>
2106 <A HREF="#pc">pcoupl</A><br>
2107 <A HREF="#pc">pcoupltype</A><br>
2108 <A HREF="#nl">periodic-molecules</A><br>
2109 <A HREF="#ewald">pme-order</A><br>
2110 <A HREF="#pull">pull</A><br>
2111 <A HREF="#pc">refcoord-scaling</A><br>
2112 <A HREF="#pc">ref-p</A><br>
2113 <A HREF="#tc">ref-t</A><br>
2114 <A HREF="#el2">rcoulomb-switch</A><br>
2115 <A HREF="#el2">rcoulomb</A><br>
2116 <A HREF="#nl">rlist</A><br>
2117 <A HREF="#nl">rlistlong</A><br>
2118 <A HREF="#tpi">rtpi</A><br>
2119 <A HREF="#vdw">rvdw-switch</A><br>
2120 <A HREF="#vdw">rvdw</A><br>
2121 <A HREF="#free">sc-alpha</A><br>
2122 <A HREF="#free">sc-power</A><br>
2123 <A HREF="#free">sc-sigma</A><br>
2124 <A HREF="#bond2">shake-tol</A><br>
2125 <A HREF="#expanded">sim-temp-low</A><br>
2126 <A HREF="#expanded">sim-temp-high</A><br>
2127 <A HREF="#expanded">simulated-tempering</A><br>
2128 <A HREF="#expanded">simulated-tempering-scaling</A><br>
2129 <A HREF="#expanded">symmetrized-transition-matrix</A><br>
2130 <A HREF="#table">table-extension</A><br>
2131 <A HREF="#pc">tau-p</A><br>
2132 <A HREF="#tc">tau-t</A><br>
2133 <A HREF="#tc">tc-grps</A><br>
2134 <A HREF="#tc">tcoupl</A><br>
2135 <A HREF="#run">tinit</A><br>
2136 <A HREF="#bond">continuation</A><br>
2137 <A HREF="#user">user1-grps</A><br>
2138 <A HREF="#user">user2-grps</A><br>
2139 <A HREF="#user">userint1</A><br>
2140 <A HREF="#user">userint2</A><br>
2141 <A HREF="#user">userint3</A><br>
2142 <A HREF="#user">userint4</A><br>
2143 <A HREF="#user">userreal1</A><br>
2144 <A HREF="#user">userreal2</A><br>
2145 <A HREF="#user">userreal3</A><br>
2146 <A HREF="#user">userreal4</A><br>
2147 <A HREF="#vdw">vdwtype</A><br>
2148 <A HREF="#vdw">vdw-modifier</A><br>
2149 <A HREF="#nl">verlet-buffer-drift</A><br>
2150 <A HREF="#out">xtc-grps</A><br>
2151 <A HREF="#out">xtc-precision</A><br>
2152 <A HREF="#sa">zero-temp-time</A><br>
2153 <A HREF="#walls">wall-atomtype</A><br>
2154 <A HREF="#walls">wall-density</A><br>
2155 <A HREF="#walls">wall-ewald-zfac</A><br>
2156 <A HREF="#walls">wall-r-linpot</A><br>
2157 <A HREF="#walls">wall-type</A><br>
2158 <A HREF="#expanded">weight-equil-count-ratio</A><br>
2159 <A HREF="#expanded">weight-equil-number-all-lambda</A><br>
2160 <A HREF="#expanded">weight-equil-number-samples</A><br>
2161 <A HREF="#expanded">weight-equil-number-steps</A><br>
2162 <A HREF="#expanded">weight-equil-wl-delta</A><br>
2163 <A HREF="#expanded">wl-ratio</A><br>
2164 <A HREF="#expanded">wl-scale</A><br>
2169 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
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