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11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdp options</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
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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> (nstlist, ns-type, pbc, periodic-molecules, rlist, rlistlong)
39 <li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
40 <li><A HREF="#vdw"><b>VdW</b></A> (vdwtype, 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, init-lambda, delta-lambda, sc-alpha, sc-power, sc-sigma, couple-moltype, couple-lambda0, couple-lambda1, couple-intramol)
55 <li><A HREF="#neq"><b>Non-equilibrium MD</b></A> (acc-grps, accelerate, freezegrps, freezedim, cos-acceleration, deform)
56 <li><A HREF="#ef"><b>Electric fields</b></A> (E-x, E-xt, E-y, E-yt, E-z, E-zt )
57 <li><A HREF="#qmmm"><b>Mixed quantum/classical dynamics</b></A> (QMMM, QMMM-grps, QMMMscheme, QMmethod, QMbasis, QMcharge, Qmmult, CASorbitals, CASelectrons, SH)
58 <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)
59 <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)
60 <li><A HREF="#user"><b>User defined thingies</b></A> (user1-grps, user2-grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
61 <li><A HREF="#idx"><b>Index</b></A>
67 <A NAME="general"><br>
71 Default values are given in parentheses. The first option in
72 the list is always the default option. Units are given in
73 square brackets The difference between a dash and an underscore
77 A <a href="mdp.html">sample <TT>.mdp</TT> file</a> is
78 available. This should be appropriate to start a normal
79 simulation. Edit it to suit your specific needs and desires. </P>
83 <h3>Preprocessing</h3>
86 <dt><b>include:</b></dt>
87 <dd>directories to include in your topology. Format:
88 <PRE>-I/home/john/mylib -I../otherlib</PRE></dd>
89 <dt><b>define:</b></dt>
90 <dd>defines to pass to the preprocessor, default is no defines. You can use
91 any defines to control options in your customized topology files. Options
92 that are already available by default are:
95 <dd>Will tell <tt>grompp</tt> to include flexible water in stead of rigid water into your
96 topology, this can be useful for normal mode analysis.</dd>
98 <dd>Will tell <tt>grompp</tt> to include posre.itp into your topology, used for
99 <!--Idx-->position restraint<!--EIdx-->s.</dd>
108 <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>
111 <dd>A leap-frog algorithm<!--QuietIdx-->leap-frog integrator<!--EQuietIdx-->
112 for integrating Newton's equations of motion.</dd>
113 <dt><b>md-vv</b></dt>
114 <dd>A velocity Verlet algorithm for integrating Newton's equations of motion.
115 For constant NVE simulations started from corresponding points in the same trajectory, the trajectories
116 are analytically, but not binary, identical to the <b>md</b> leap-frog integrator. The the kinetic
117 energy, which is determined from the whole step velocities and is therefore
118 slightly too high. The advantage of this integrator is more accurate,
119 reversible Nose-Hoover and Parrinello-Rahman coupling integration
120 based on Trotter expansion, as well as (slightly too small) full step velocity
121 output. This all comes at the cost off extra computation, especially with
122 constraints and extra communication in parallel. Note that for nearly all
123 production simulations the <b>md</b> integrator is accurate enough.
125 <dt><b>md-vv-avek</b></dt>
126 <dd>A velocity Verlet algorithm identical to <b>md-vv</b>, except that
127 the kinetic energy is determined as the average of
128 the two half step kinetic energies as in the <b>md</b> integrator, and this thus more accurate.
129 With Nose-Hoover and/or Parrinello-Rahman coupling this comes with
130 a slight increase in computational cost.
133 <dd> An accurate leap-frog stochastic dynamics integrator.
134 Four Gaussian random number are required
135 per integration step per degree of freedom. With constraints,
136 coordinates needs to be constrained twice per integration step.
137 Depending on the computational cost of the force calculation,
138 this can take a significant part of the simulation time.
139 The temperature for one or more groups of atoms
140 (<b><A HREF="#tc">tc-grps</A></b>)
141 is set with <b><A HREF="#tc">ref-t</A></b> [K],
142 the inverse friction constant for each group is set with
143 <b><A HREF="#tc">tau-t</A></b> [ps].
144 The parameter <b><A HREF="#tc">tcoupl</A></b> is ignored.
145 The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.
146 When used as a thermostat, an appropriate value for <b>tau-t</b> is 2 ps,
147 since this results in a friction that is lower than the internal friction
148 of water, while it is high enough to remove excess heat
149 (unless <b>cut-off</b> or <b>reaction-field</b> electrostatics is used).
150 NOTE: temperature deviations decay twice as fast as with
151 a Berendsen thermostat with the same <b>tau-t</b>.</dd>
153 <dd> An efficient leap-frog stochastic dynamics integrator.
154 This integrator is equivalent to <b>sd</b>, except that it requires
155 only one Gaussian random number and one constraint step and is therefore
156 significantly faster. Without constraints the accuracy is the same as <b>sd</b>.
157 With constraints the accuracy is significantly reduced, so then <b>sd</b>
158 will often be preferred.</dd>
160 <dd>An Euler integrator for Brownian or position Langevin dynamics, the
161 velocity is the force divided by a friction coefficient
162 (<b><A HREF="#ld">bd-fric</A></b> [amu ps<sup>-1</sup>])
163 plus random thermal noise (<b><A HREF="#tc">ref-t</A></b>).
164 When <b><A HREF="#ld">bd-fric</A></b><tt>=0</tt>, the friction coefficient for each
165 particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>, as for the
166 integrator <tt>sd</tt>.
167 The random generator is initialized with <b><A HREF="#ld">ld-seed</A></b>.</dd>
169 <dt><b>steep</b></dt>
170 <dd>A <!--Idx-->steepest descent<!--EIdx--> algorithm for energy
171 minimization. The maximum step size is <b><A HREF="#em">emstep</A></b>
172 [nm], the tolerance is <b><A HREF="#em">emtol</A></b> [kJ
173 mol<sup>-1</sup> nm<sup>-1</sup>].</dd>
175 <dd>A <!--Idx-->conjugate gradient<!--EIdx--> algorithm for energy
176 minimization, the tolerance is <b>emtol</b> [kJ mol<sup>-1</sup>
177 nm<sup>-1</sup>]. CG is more efficient when a steepest descent step
178 is done every once in a while, this is determined by
179 <b><A HREF="#em">nstcgsteep</A></b>.
180 For a minimization prior to a normal mode analysis, which requires
181 a very high accuracy, GROMACS should be compiled in double precision.</dd>
182 <dt><b>l-bfgs</b></dt>
183 <dd>A <!--Idx-->quasi-Newtonian<!--EIdx--> algorithm for energy minimization
184 according to the low-memory Broyden-Fletcher-Goldfarb-Shanno approach.
185 In practice this seems to converge faster than Conjugate Gradients, but due
186 to the correction steps necessary it is not (yet) parallelized.
189 <dd>Normal mode analysis<!--QuietIdx-->normal-mode analysis<!--EQuietIdx--> is performed
190 on the structure in the <tt>tpr</tt> file. GROMACS should be
191 compiled in double precision.</dd>
193 <dd> Test particle insertion. The last molecule in the topology
194 is the test particle. A trajectory should be provided with
195 the <tt>-rerun</tt> option of <tt>mdrun</tt>. This trajectory
196 should not contain the molecule to be inserted. Insertions
197 are performed <b>nsteps</b> times in each frame at random locations
198 and with random orientiations of the molecule. When <b>nstlist</b>
199 is larger than one, <b>nstlist</b> insertions are performed
200 in a sphere with radius <b><A HREF="#tpi">rtpi</A></b>
201 around a the same random location using the same neighborlist
202 (and the same long-range energy when <b>rvdw</b> or <b>rcoulomb</b>><b>rlist</b>,
203 which is only allowed for single-atom molecules).
204 Since neighborlist construction is expensive, one can perform several
205 extra insertions with the same list almost for free.
206 The random seed is set with <b><A HREF="#ld">ld-seed</A></b>.
207 The temperature for the Boltzmann weighting is set with
208 <b><A HREF="#tc">ref-t</A></b>, this should match the temperature
209 of the simulation of the original trajectory.
210 Dispersion correction is implemented correctly for tpi.
211 All relevant quantities are written to the file specified with
212 the <tt>-tpi</tt> option of <tt>mdrun</tt>.
213 The distribution of insertion energies is written to the file specified with
214 the <tt>-tpid</tt> option of <tt>mdrun</tt>.
215 No trajectory or energy file is written.
216 Parallel tpi gives identical results to single node tpi.
217 For charged molecules, using PME with a fine grid is most accurate
218 and also efficient, since the potential in the system only needs
219 to be calculated once per frame.
222 <dd> Test particle insertion into a predefined cavity location.
223 The procedure is the same as for <b>tpi</b>, except that one coordinate
224 extra is read from the trajectory, which is used as the insertion location.
225 The molecule to be inserted should be centered at 0,0,0. Gromacs does
226 not do this for you, since for different situations a different
227 way of centering might be optimal.
228 Also <b><A HREF="#tpi">rtpi</A></b> sets the radius for the sphere
229 around this location. Neighbor searching is done only once per frame,
230 <b>nstlist</b> is not used.
231 Parallel tpic gives identical results to single node tpic.
234 <dt><b>tinit: (0) [ps]</b></dt>
235 <dd>starting time for your run (only makes sense for integrators <tt>md</tt>,
236 <tt>sd</tt> and <tt>bd</tt>)</dd>
237 <dt><b>dt: (0.001) [ps]</b></dt></dd>
238 <dd>time step for integration (only makes sense for integrators <tt>md</tt>,
239 <tt>sd</tt> and <tt>bd</tt>)</dd>
240 <dt><b>nsteps: (0)</b></dt>
241 <dd>maximum number of steps to integrate or minimize, -1 is no maximum</dd>
242 <dt><b>init-step: (0)</b></dt>
243 <dd>The starting step.
244 The time at an step i in a run is calculated as: t = <tt>tinit</tt> + <tt>dt</tt>*(<tt>init-step</tt> + i).
245 The free-energy lambda is calculated as: lambda = <tt>init-lambda</tt> + <tt>delta-lambda</tt>*(<tt>init-step</tt> + i).
246 Also non-equilibrium MD parameters can depend on the step number.
247 Thus for exact restarts or redoing part of a run it might be necessary to
248 set <tt>init-step</tt> to the step number of the restart frame.
249 <tt>tpbconv</tt> does this automatically.
251 <dt><b>comm-mode:</b></dt>
253 <dt><b>Linear</b></dt>
254 <dd>Remove center of mass translation</dd>
255 <dt><b>Angular</b></dt>
256 <dd>Remove center of mass translation and rotation around the center of mass
259 <dd>No restriction on the center of mass motion
261 <dt><b>nstcomm: (10) [steps]</b></dt>
262 <dd>frequency for center of mass motion removal</dd>
263 <dt><b>comm-grps:</b></dt>
264 <dd>group(s) for center of mass motion removal, default is the whole system</dd>
269 <h3><!--Idx-->Langevin dynamics<!--EIdx--></h3>
272 <dt><b>bd-fric: (0) [amu ps<sup>-1</sup>]</b></dt>
273 <dd>Brownian dynamics friction coefficient.
274 When <b>bd-fric</b><tt>=0</tt>, the friction coefficient for each
275 particle is calculated as mass/<b><A HREF="#tc">tau-t</A></b>.</dd>
276 <dt><b>ld-seed: (1993) [integer]</b></dt>
277 <dd>used to initialize random generator for thermal noise
278 for stochastic and Brownian dynamics.
279 When <b>ld-seed</b> is set to -1, the seed is calculated from the process ID.
280 When running BD or SD on multiple processors, each processor uses a seed equal
281 to <b>ld-seed</b> plus the processor number.</dd>
286 <h3>Energy minimization<!--QuietIdx-->energy minimization<!--EQuietIdx--></h3>
288 <dt><b>emtol: (10.0) [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
289 <dd>the minimization is converged when the maximum force is smaller than
291 <dt><b>emstep: (0.01) [nm]</b></dt>
292 <dd>initial step-size</dd>
293 <dt><b>nstcgsteep: (1000) [steps]</b></dt>
294 <dd>frequency of performing 1 steepest descent step while doing
295 conjugate gradient energy minimization.</dd>
296 <dt><b>nbfgscorr: (10)</b></dt>
297 <dd>Number of correction steps to use for L-BFGS minimization. A higher
298 number is (at least theoretically) more accurate, but slower.</dd>
301 <A NAME="xmdrun"><br>
303 <h3>Shell Molecular Dynamics<!--QuietIdx-->shell molecular dynamics<!--EQuietIdx--></h3>
305 flexible constraints are present in the system the positions of the shells
306 and the lengths of the flexible constraints are optimized at
307 every time step until either the RMS force on the shells and constraints
308 is less than emtol, or a maximum number of iterations (niter) has been reached
310 <dt><b>emtol: (10.0) [kJ mol<sup>-1</sup> nm<sup>-1</sup>]</b></dt>
311 <dd>the minimization is converged when the maximum force is smaller than
312 this value. For shell MD this value should be 1.0 at most, but since the
313 variable is used for energy minimization as well the default is 10.0.</dd>
314 <dt><b>niter: (20)</b></dt>
315 <dd>maximum number of iterations for optimizing the shell positions
316 and the flexible constraints.</dd>
317 <dt><b>fcstep: (0) [ps<sup>2</sup>]</b></dt>
318 <dd>the step size for optimizing the flexible constraints.
319 Should be chosen as mu/(d<sup>2</sup>V/dq<sup>2</sup>)
320 where mu is the reduced mass of two particles in a flexible constraint
321 and d<sup>2</sup>V/dq<sup>2</sup> is the second derivative of the potential
322 in the constraint direction. Hopefully this number does not differ too
323 much between the flexible constraints, as the number of iterations
324 and thus the runtime is very sensitive to <tt>fcstep</tt>.
325 Try several values!</dd>
330 <h3>Test particle insertion</h3>
332 <dt><b>rtpi: (0.05) [nm]</b></dt>
333 <dd>the test particle insertion radius see integrators
334 <b><a href="#run">tpi</a></b> and <b><a href="#run">tpic</a></b></dd>
339 <h3>Output control</h3>
341 <dt><b>nstxout: (0) [steps]</b></dt>
342 <dd>frequency to write coordinates to output
343 <!--Idx-->trajectory file<!--EIdx-->, the last coordinates are always written</dd>
344 <dt><b>nstvout: (0) [steps]</b></dt>
345 <dd>frequency to write velocities to output trajectory,
346 the last velocities are always written</dd>
347 <dt><b>nstfout: (0) [steps]</b></dt>
348 <dd>frequency to write forces to output trajectory.</dd>
349 <dt><b>nstlog: (1000) [steps]</b></dt>
350 <dd>frequency to write energies to <!--Idx-->log file<!--EIdx-->,
351 the last energies are always written</dd>
352 <dt><b>nstcalcenergy: (-1)</b></dt>
353 <dd>frequency for calculating the energies, 0 is never.
354 This option is only relevant with dynamics.
355 With a twin-range cut-off setup <b>nstcalcenergy</b> should be equal to
356 or a multiple of <b>nstlist</b>.
357 This option affects the performance in parallel simulations,
358 because calculating energies requires global communication between all
359 processes which can become a bottleneck at high parallelization.
360 The default value of -1 sets <b>nstcalcenergy</b> equal to <b>nstlist</b>,
361 unless <b>nstlist</b> ≤0, then a value of 10 is used.
362 If <b>nstenergy</b> is smaller than the automatically generated value,
363 the lowest common denominator of <b>nstenergy</b> and <b>nstlist</b> is used.
365 <dt><b>nstenergy: (100) [steps]</b></dt>
366 <dd>frequency to write energies to energy file,
367 the last energies are always written,
368 should be a multiple of <b>nstcalcenergy</b>.
369 Note that the exact sums and fluctuations over all MD steps
370 modulo <b>nstcalcenergy</b> are stored in the energy file,
371 so <tt>g_energy</tt> can report exact
372 energy averages and fluctuations also when <b>nstenergy</b><tt>>1</tt></dd>
373 <dt><b>nstxtcout: (0) [steps]</b></dt>
374 <dd>frequency to write coordinates to xtc trajectory</dd>
375 <dt><b>xtc-precision: (1000) [real]</b></dt>
376 <dd>precision to write to xtc trajectory</dd>
377 <dt><b>xtc-grps:</b></dt>
378 <dd>group(s) to write to xtc trajectory, default the whole system is written
379 (if <b>nstxtcout</b> > 0)</dd>
380 <dt><b>energygrps:</b></dt>
381 <dd>group(s) to write to energy file</dd>
386 <h3>Neighbor searching<!--QuietIdx-->neighbor searching<!--EQuietIdx--></h3>
388 <dt><b>nstlist: (10) [steps]</b></dt>
390 <dt><b>>0</b></dt>
391 <dd>Frequency to update the <!--Idx-->neighbor list<!--EIdx--> (and
392 the long-range forces, when using twin-range cut-offs). When this is 0,
393 the neighbor list is made only once.
394 With energy minimization the neighborlist will be updated for every
395 energy evaluation when <b>nstlist</b><tt>>0</tt>.</dd>
397 <dd>The neighbor list is only constructed once and never updated.
398 This is mainly useful for vacuum simulations in which all particles
401 <dd>Automated update frequency.
402 This can only be used with switched, shifted or user potentials where
403 the cut-off can be smaller than <b>rlist</b>. One then has a buffer
404 of size <b>rlist</b> minus the longest cut-off.
405 The neighbor list is only updated when one or more particles have moved further
406 than half the buffer size from the center of geometry of their charge group
407 as determined at the previous neighbor search.
408 Coordinate scaling due to pressure coupling or the <b>deform</b> option
409 is taken into account.
410 This option guarantees that their are no cut-off artifacts,
411 but for larger systems this can come at a high computational cost,
412 since the neighbor list update frequency will be determined
413 by just one or two particles moving slightly beyond the half buffer length
414 (which does not necessarily imply that the neighbor list is invalid),
415 while 99.99% of the particles are fine.
419 <dt><b>ns-type:</b></dt>
422 <dd>Make a grid in the box and only check atoms in neighboring grid
423 cells when constructing a new neighbor list every <b>nstlist</b> steps.
424 In large systems grid search is much faster than simple search.</dd>
425 <dt><b>simple</b></dt>
426 <dd>Check every atom in the box when constructing a new neighbor list
427 every <b>nstlist</b> steps.</dd>
433 <dd>Use periodic boundary conditions in all directions.</dd>
435 <dd>Use no periodic boundary conditions, ignore the box.
436 To simulate without cut-offs, set all cut-offs to 0 and <b>nstlist</b><tt>=0</tt>.
437 For best performance without cut-offs, use <b>nstlist</b><tt>=0</tt>,
438 <b>ns-type</b><tt>=simple</tt>
439 and particle decomposition instead of domain decomposition.</dd>
441 <dd>Use periodic boundary conditions in x and y directions only.
442 This works only with <b>ns-type</b><tt>=grid</tt> and can be used
443 in combination with <b><a href="#walls">walls</a></b>.
444 Without walls or with only one wall the system size is infinite
445 in the z direction. Therefore pressure coupling or Ewald summation
446 methods can not be used.
447 These disadvantages do not apply when two walls are used.</dd>
450 <dt><b>periodic-molecules:</b></dt>
453 <dd>molecules are finite, fast molecular PBC can be used</dd>
455 <dd>for systems with molecules that couple to themselves through
456 the periodic boundary conditions, this requires a slower PBC algorithm
457 and molecules are not made whole in the output</dd>
460 <dt><b>rlist: (1) [nm]</b></dt>
461 <dd>cut-off distance for the short-range neighbor list</dd>
463 <dt><b>rlistlong: (-1) [nm]</b></dt>
464 <dd>Cut-off distance for the long-range neighbor list.
465 This parameter is only relevant for a twin-range cut-off setup
466 with switched potentials. In that case a buffer region is required to account
467 for the size of charge groups. In all other cases this parameter
468 is automatically set to the longest cut-off distance.</dd>
474 <h3>Electrostatics<!--QuietIdx-->electrostatics<!--EQuietIdx--></h3>
476 <dt><b>coulombtype:</b></dt>
479 <dt><b>Cut-off</b></dt>
480 <dd>Twin range cut-offs with neighborlist cut-off <b>rlist</b> and
481 Coulomb cut-off <b>rcoulomb</b>,
482 where <b>rcoulomb</b>≥<b>rlist</b>.
484 <dt><b>Ewald</b></dt>
485 <dd>Classical <!--Idx-->Ewald sum<!--EIdx--> electrostatics.
486 The real-space cut-off <b>rcoulomb</b> should be equal to <b>rlist</b>.
487 Use e.g. <b>rlist</b><tt>=0.9</tt>, <b>rcoulomb</b><tt>=0.9</tt>. The highest magnitude of
488 wave vectors used in reciprocal space is controlled by <b>fourierspacing</b>.
489 The relative accuracy of direct/reciprocal space
490 is controlled by <b>ewald-rtol</b>.
492 NOTE: Ewald scales as O(N<sup>3/2</sup>)
493 and is thus extremely slow for large systems. It is included mainly for
494 reference - in most cases PME will perform much better.</dd>
496 <dt><b><!--Idx-->PME<!--EIdx--></b></dt>
497 <dd>Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct space is similar
498 to the Ewald sum, while the reciprocal part is performed with
499 FFTs. Grid dimensions are controlled with <b>fourierspacing</b> and the
500 interpolation order with <b>pme-order</b>. With a grid spacing of 0.1
501 nm and cubic interpolation the electrostatic forces have an accuracy
502 of 2-3*10<sup>-4</sup>. Since the error from the vdw-cutoff is larger than this you
503 might try 0.15 nm. When running in parallel the interpolation
504 parallelizes better than the FFT, so try decreasing grid dimensions
505 while increasing interpolation.</dd>
507 <dt><b><!--Idx-->P3M-AD<!--EIdx--></b></dt>
508 <dd>Particle-Particle Particle-Mesh algorithm with analytical derivative
509 for for long range electrostatic interactions. The method and code
510 is identical to SPME, except that the influence function is optimized
511 for the grid. This gives a slight increase in accuracy.</dd>
513 <dt><b>Reaction-Field electrostatics<!--QuietIdx-->reaction-field electrostatics<!--EQuietIdx--></b></dt>
514 <dd>Reaction field with Coulomb cut-off <b>rcoulomb</b>,
515 where <b>rcoulomb</b> ≥ <b>rlist</b>.
516 The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
517 The dielectric constant can be set to infinity by setting <b>epsilon-rf</b><tt>=0</tt>.</dd>
519 <dt><b>Generalized-Reaction-Field</b></dt>
520 <dd>Generalized reaction field with Coulomb cut-off <b>rcoulomb</b>,
521 where <b>rcoulomb</b> ≥ <b>rlist</b>.
522 The dielectric constant beyond the cut-off is <b>epsilon-rf</b>.
523 The ionic strength is computed from the number of charged
524 (i.e. with non zero charge) <!--Idx-->charge group<!--EIdx-->s.
525 The temperature for the GRF potential is set with
526 <b><A HREF="#tc">ref-t</A></b> [K].</dd>
528 <dt><b>Reaction-Field-zero</b></dt>
529 <dd>In GROMACS normal reaction-field electrostatics leads to bad
530 energy conservation. <b>Reaction-Field-zero</b> solves this
531 by making the potential zero beyond the cut-off. It can only
532 be used with an infinite dielectric constant (<b>epsilon-rf=0</b>),
533 because only for that value the force vanishes at the cut-off.
534 <b>rlist</b> should be 0.1 to 0.3 nm larger than <b>rcoulomb</b>
535 to accommodate for the size of charge groups and diffusion
536 between neighbor list updates. This, and the fact that table lookups
537 are used instead of analytical functions make <b>Reaction-Field-zero</b>
538 computationally more expensive than normal reaction-field.</dd>
540 <dt><b>Reaction-Field-nec</b></dt>
541 <dd>The same as <b>Reaction-Field</b>, but implemented as in
542 GROMACS versions before 3.3. No reaction-field correction is applied
543 to excluded atom pairs and self pairs.
544 The 1-4 interactions are calculated using a reaction-field.
545 The missing correction due to the excluded pairs that do not have a 1-4
546 interaction is up to a few percent of the total electrostatic
547 energy and causes a minor difference in the forces and the pressure.</dd>
549 <dt><b>Shift</b></dt>
550 <dd>Analogous to <b>Shift</b> for <b>vdwtype</b>.
551 You might want to use <b>Reaction-Field-zero</b> instead,
552 which has a similar potential shape, but has a physical interpretation
553 and has better energies due to the exclusion correction terms.
556 <dt><b>Encad-Shift</b></dt>
558 potential is decreased over the whole range, using the definition
559 from the Encad simulation package.</dd>
561 <dt><b>Switch</b></dt>
562 <dd>Analogous to <b>Switch</b> for <b>vdwtype</b>.
563 Switching the Coulomb potential can lead to serious artifacts,
564 advice: use <b>Reaction-Field-zero</b> instead.</dd>
567 <dd><a name="usertab"></a><tt>mdrun</tt> will now expect to find a file
568 <tt>table.xvg</tt> with user-defined potential functions for
569 repulsion, dispersion and Coulomb. When pair interactions are present,
570 <tt>mdrun</tt> also expects to find a file <tt>tablep.xvg</tt> for
571 the pair interactions. When the same interactions should be used
572 for non-bonded and pair interactions the user can specify the same
573 file name for both table files.
574 These files should contain 7
575 columns: the <tt>x</tt> value,
576 <tt>f(x)</tt>, <tt>-f'(x)</tt>,
577 <tt>g(x)</tt>, <tt>-g'(x)</tt>,
578 <tt>h(x)</tt>, <tt>-h'(x)</tt>,
579 where <tt>f(x)</tt> is the Coulomb function, <tt>g(x)</tt> the dispersion function
580 and <tt>h(x)</tt> the repulsion function.
581 When <b>vdwtype</b> is not set to <b>User</b> the values
582 for <tt>g</tt>, <tt>-g'</tt>, <tt>h</tt> and <tt>-h'</tt> are ignored.
583 For the non-bonded interactions <tt>x</tt> values should run
584 from 0 to the largest cut-off distance + <b>table-extension</b>
585 and should be uniformly spaced. For the pair interactions the table
586 length in the file will be used.
587 The optimal spacing, which is used for non-user tables,
588 is <tt>0.002</tt> [nm] when you run in single precision
589 or <tt>0.0005</tt> [nm] when you run in double precision.
590 The function value at <tt>x=0</tt> is not important. More information is
591 in the printed manual.</dd>
593 <dt><b>PME-Switch</b></dt>
594 <dd>A combination of PME and a switch function for the direct-space part
595 (see above). <b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
596 This is mainly useful constant energy simulations. For constant temperature
597 simulations the advantage of improved energy conservation
598 is usually outweighed by the small loss in accuracy of the electrostatics.
601 <dt><b>PME-User</b></dt>
602 <dd>A combination of PME and user tables (see above).
603 <b>rcoulomb</b> is allowed to be smaller than <b>rlist</b>.
604 The PME mesh contribution is subtracted from the user table by <tt>mdrun</tt>.
605 Because of this subtraction the user tables should contain
606 about 10 decimal places.</dd>
608 <dt><b>PME-User-Switch</b></dt>
609 <dd>A combination of PME-User and a switching function (see above).
610 The switching function is applied to final particle-particle interaction,
611 i.e. both to the user supplied function and the PME Mesh correction part.</dd>
616 <dt><b>rcoulomb-switch: (0) [nm]</b></dt>
617 <dd>where to start switching the Coulomb potential</dd>
619 <dt><b>rcoulomb: (1) [nm]</b></dt>
620 <dd>distance for the Coulomb <!--Idx-->cut-off<!--EIdx--></dd>
622 <dt><b>epsilon-r: (1)</b></dt>
623 <dd>The relative <!--Idx-->dielectric constant<!--EIdx-->.
624 A value of 0 means infinity.</dd>
626 <dt><b>epsilon-rf: (0)</b></dt>
627 <dd>The relative dielectric constant of the reaction field.
628 This is only used with reaction-field electrostatics.
629 A value of 0 means infinity.</dd>
636 <dt><b>vdwtype:</b></dt>
638 <dt><b>Cut-off</b></dt>
639 <dd>Twin range cut-offs with neighbor list cut-off <b>rlist</b> and
640 VdW cut-off <b>rvdw</b>,
641 where <b>rvdw</b> <tt>≥</tt> <b>rlist</b>.</dd>
642 <dt><b>Shift</b></dt>
643 <dd>The LJ (not Buckingham) potential is decreased over the whole
644 range and the forces decay smoothly to zero between <b>rvdw-switch</b>
645 and <b>rvdw</b>. The neighbor search cut-off <b>rlist</b> should be
646 0.1 to 0.3 nm larger than <b>rvdw</b> to accommodate for the size of
647 charge groups and diffusion between neighbor list
650 <dt><b>Switch</b></dt>
651 <dd>The LJ (not Buckingham)
652 potential is normal out to <b>rvdw-switch</b>, after which it is switched
653 off to reach zero at <b>rvdw</b>. Both the potential and force functions
654 are continuously smooth, but be aware that all switch functions will give rise
655 to a bulge (increase) in the force (since we are switching the potential).
656 The neighbor search cut-off <b>rlist</b> should be 0.1 to 0.3 nm larger than
657 <b>rvdw</b> to accommodate for the size of charge groups and diffusion
658 between neighbor list updates.</dd>
660 <dt><b>Encad-Shift</b></dt>
661 <dd>The LJ (not Buckingham)
662 potential is decreased over the whole range, using the definition
663 from the Encad simulation package.</dd>
666 <dd>See <b><a href="#usertab">user</a></b> for <b>coulombtype</b>.
667 The function value at <tt>x=0</tt> is not important. When you want to
668 use LJ correction, make sure that <b>rvdw</b> corresponds to the
669 cut-off in the user-defined function.
670 When <b>coulombtype</b> is not set to <b>User</b> the values
671 for <tt>f</tt> and <tt>-f'</tt> are ignored.</dd>
674 <dt><b>rvdw-switch: (0) [nm]</b></dt>
675 <dd>where to start switching the LJ potential</dd>
677 <dt><b>rvdw: (1) [nm]</b></dt>
678 <dd>distance for the LJ or Buckingham <!--Idx-->cut-off<!--EIdx--></dd>
680 <dt><b>DispCorr:</b></dt>
681 <dd><dl compact></dd>
683 <dd>don't apply any correction</dd>
684 <dt><b>EnerPres</b></dt>
685 <dd>apply long range <!--Idx-->dispersion correction<!--EIdx-->s for Energy
688 <dd>apply long range dispersion corrections for Energy
697 <dt><b>table-extension: (1) [nm]</b></dt>
698 <dd>Extension of the non-bonded potential lookup tables beyond the largest cut-off distance.
699 The value should be large enough to account for charge group sizes
700 and the diffusion between neighbor-list updates.
701 Without user defined potential the same table length is used
702 for the lookup tables for the 1-4 interactions,
703 which are always tabulated irrespective of the use of
704 tables for the non-bonded interactions. </dd>
706 <dt><b>energygrp-table:</b></dt>
707 <dd>When user tables are used for electrostatics and/or VdW,
708 here one can give pairs of energy groups for which seperate
709 user tables should be used.
710 The two energy groups will be appended to the table file name,
711 in order of their definition in <b>energygrps</b>, seperated by underscores.
712 For example, if <tt>energygrps = Na Cl Sol</tt>
713 and <tt>energygrp-table = Na Na Na Cl</tt>, <tt>mdrun</tt> will read
714 <tt>table_Na_Na.xvg</tt> and <tt>table_Na_Cl.xvg</tt> in addition
715 to the normal <tt>table.xvg</tt> which will be used for all other
724 <dt><b>fourierspacing: (0.12) [nm]</b></dt>
725 <dd>For ordinary Ewald, the ratio of the box dimensions and the spacing
726 determines a lower bound for the number of wave vectors to use in each
727 (signed) direction. For PME and P3M, that ratio determines a lower bound
728 for the number of Fourier-space grid points that will be used along that
729 axis. In all cases, the number for each direction can be overridden by
730 entering a non-zero value for <b>fourier_n[xyz]</b>.
731 For optimizing the relative load of the particle-particle interactions
732 and the mesh part of PME, it is useful to know that
733 the accuracy of the electrostatics remains nearly constant
734 when the Coulomb cut-off and the PME grid spacing are scaled
735 by the same factor.</dd>
737 <dt><b>fourier-nx (0) ; fourier-ny (0) ; fourier-nz: (0)</b></dt>
738 <dd>Highest magnitude of wave vectors in reciprocal space when using Ewald.</dd>
739 <dd>Grid size when using PME or P3M. These values override
740 <b>fourierspacing</b> per direction. The best choice is powers of
741 2, 3, 5 and 7. Avoid large primes.</dd>
743 <dt><b>pme-order (4)</b></dt>
744 <dd>Interpolation order for PME. 4 equals cubic interpolation. You might try
745 6/8/10 when running in parallel and simultaneously decrease grid dimension.</dd>
747 <dt><b>ewald-rtol (1e-5)</b></dt>
748 <dd>The relative strength of the Ewald-shifted direct potential at
749 <b>rcoulomb</b> is given by <b>ewald-rtol</b>.
750 Decreasing this will give a more accurate direct sum,
751 but then you need more wave vectors for the reciprocal sum.</dd>
753 <dt><b>ewald-geometry: (3d)</b></dt>
756 <dd>The Ewald sum is performed in all three dimensions.</dd>
758 <dd>The reciprocal sum is still performed in 3D,
759 but a force and potential correction applied in the <tt>z</tt>
760 dimension to produce a pseudo-2D summation.
761 If your system has a slab geometry in the <tt>x-y</tt> plane you can
762 try to increase the <tt>z</tt>-dimension of the box (a box height of 3 times
763 the slab height is usually ok)
764 and use this option.</dd>
767 <dt><b>epsilon-surface: (0)</b></dt>
768 <dd>This controls the dipole correction to the Ewald summation in 3D. The
769 default value of zero means it is turned off. Turn it on by setting it to the value
770 of the relative permittivity of the imaginary surface around your infinite system. Be
771 careful - you shouldn't use this if you have free mobile charges in your system.
772 This value does not affect the slab 3DC variant of the long range corrections.</dd>
775 <dt><b>optimize-fft:</b></dt>
778 <dd>Don't calculate the optimal FFT plan for the grid at startup.</dd>
780 <dd>Calculate the optimal FFT plan for the grid at startup. This saves a
781 few percent for long simulations, but takes a couple of minutes
789 <h3>Temperature coupling<!--QuietIdx-->temperature coupling<!--EQuietIdx--></h3>
792 <dt><b>tcoupl:</b></dt>
795 <dd>No temperature coupling.</dd>
796 <dt><b>berendsen</b></dt>
797 <dd>Temperature coupling with a Berendsen-thermostat to a bath with
798 temperature <b>ref-t</b> [K], with time constant <b>tau-t</b> [ps].
799 Several groups can be coupled separately, these are specified in the
800 <b>tc-grps</b> field separated by spaces.</dd>
801 <dt><b>nose-hoover</b></dt>
802 <dd>Temperature coupling using a Nose-Hoover extended
803 ensemble. The reference temperature and coupling groups are selected
804 as above, but in this case <b>tau-t</b> [ps] controls the period
805 of the temperature fluctuations at equilibrium, which is slightly
806 different from a relaxation time.
807 For NVT simulations the conserved energy quantity is written
808 to energy and log file.</dd>
809 <dt><b>v-rescale</b></dt>
810 <dd>Temperature coupling using velocity rescaling with a stochastic term
812 This thermostat is similar to Berendsen coupling, with the same scaling
813 using <b>tau-t</b>, but the stochastic term ensures that a proper
814 canonical ensemble is generated. The random seed is set with
815 <b><A HREF="#ld">ld-seed</A></b>.
816 This thermostat works correctly even for <b>tau-t</b><tt>=0</tt>.
817 For NVT simulations the conserved energy quantity is written
818 to the energy and log file.</dd>
820 <dt><b>nsttcouple: (-1)</b></dt>
821 <dd>The frequency for coupling the temperature.
822 The default value of -1 sets <b>nsttcouple</b> equal to <b>nstlist</b>,
823 unless <b>nstlist</b>≤0, then a value of 10 is used.
824 For velocity Verlet integrators <b>nsttcouple</b> is set to 1.</dd>
826 <dt><b>nh-chain-length (10)</b></dt>
827 <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>
828 <dt><b>tc-grps:</b></dt>
829 <dd>groups to couple separately to temperature bath</dd>
830 <dt><b>tau-t: [ps]</b></dt>
831 <dd>time constant for coupling (one for each group in <b>tc-grps</b>),
832 -1 means no temperature coupling</dd>
833 <dt><b>ref-t: [K]</b></dt>
834 <dd>reference temperature for coupling (one for each group in <b>tc-grps</b>)</dd>
839 <h3>Pressure coupling<!--QuietIdx-->pressure coupling<!--EQuietIdx--></h3>
842 <dt><b>pcoupl:</b></dt>
845 <dd>No pressure coupling. This means a fixed box size.</dd>
846 <dt><b>berendsen</b></dt>
847 <dd>Exponential relaxation pressure coupling with time constant
848 <b>tau-p</b> [ps]. The box is scaled every timestep. It has been
849 argued that this does not yield a correct thermodynamic ensemble,
850 but it is the most efficient way to scale a box at the beginning
852 <dt><b>Parrinello-Rahman</b></dt>
853 <dd>Extended-ensemble pressure coupling where the box vectors are
854 subject to an equation of motion. The equation of motion for the atoms
855 is coupled to this. No instantaneous scaling takes place. As for
856 Nose-Hoover temperature coupling the time constant <b>tau-p</b> [ps]
857 is the period of pressure fluctuations at equilibrium. This is
858 probably a better method when you want to apply pressure scaling
859 during data collection, but beware that you can get very large
860 oscillations if you are starting from a different pressure. For
861 simulations where the exact fluctation of the NPT ensemble are
862 important, or if the pressure coupling time is very short it may not
863 be appropriate, as the previous time step pressure is used in some
864 steps of the GROMACS implementation for the current time step pressure.</dd>
867 <dd>Martyna-Tuckerman-Tobias-Klein implementation, only useable with <b>md-vv</b>
868 or <b>md-vv-avek</b>, very similar to Parrinello-Rahman.
869 As for Nose-Hoover temperature coupling the time constant <b>tau-p</b>
870 [ps] is the period of pressure fluctuations at equilibrium. This is
871 probably a better method when you want to apply pressure scaling
872 during data collection, but beware that you can get very large
873 oscillations if you are starting from a different pressure. Currently only supports isotropic scaling.</dd>
877 <dt><b>pcoupltype:</b></dt>
879 <dt><b>isotropic</b></dt>
880 <dd>Isotropic pressure coupling with time constant <b>tau-p</b> [ps].
881 The compressibility and reference pressure are set with
882 <b>compressibility</b> [bar<sup>-1</sup>] and <b>ref-p</b> [bar], one
883 value is needed.</dd>
884 <dt><b>semiisotropic</b></dt>
885 <dd>Pressure coupling which is isotropic in the <tt>x</tt> and <tt>y</tt> direction,
886 but different in the <tt>z</tt> direction.
887 This can be useful for membrane simulations.
888 2 values are needed for <tt>x/y</tt> and <tt>z</tt> directions respectively.</dd>
889 <dt><b>anisotropic</b></dt>
890 <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>
891 components, respectively.
892 When the off-diagonal compressibilities are set to zero,
893 a rectangular box will stay rectangular.
894 Beware that anisotropic scaling can lead to extreme deformation
895 of the simulation box.</dd>
896 <dt><b>surface-tension</b></dt>
897 <dd>Surface tension coupling for surfaces parallel to the xy-plane.
898 Uses normal pressure coupling for the <tt>z</tt>-direction, while the surface tension
899 is coupled to the <tt>x/y</tt> dimensions of the box.
900 The first <b>ref-p</b> value is the reference surface tension times
901 the number of surfaces [bar nm],
902 the second value is the reference <tt>z</tt>-pressure [bar].
903 The two <b>compressibility</b> [bar<sup>-1</sup>] values are the compressibility
904 in the <tt>x/y</tt> and <tt>z</tt> direction respectively.
905 The value for the <tt>z</tt>-compressibility should be reasonably accurate since it
906 influences the convergence of the surface-tension, it can also be set to zero
907 to have a box with constant height.</dd>
910 <dt><b>nstpcouple: (-1)</b></dt>
911 <dd>The frequency for coupling the pressure.
912 The default value of -1 sets <b>nstpcouple</b> equal to <b>nstlist</b>,
913 unless <b>nstlist</b> ≤0, then a value of 10 is used.
914 For velocity Verlet integrators <b>nstpcouple</b> is set to 1.</dd>
917 <dt><b>tau-p: (1) [ps]</b></dt>
918 <dd>time constant for coupling</dd>
919 <dt><b>compressibility: [bar<sup>-1</sup>]</b></dt>
920 <dd>compressibility (NOTE: this is now really in bar<sup>-1</sup>)
921 For water at 1 atm and 300 K the compressibility is 4.5e-5 [bar<sup>-1</sup>].</dd>
922 <dt><b>ref-p: [bar]</b></dt>
923 <dd>reference pressure for coupling</dd>
924 <dt><b>refcoord-scaling:</b></dt>
927 <dd>The reference coordinates for position restraints are not modified.
928 Note that with this option the virial and pressure will depend on the absolute
929 positions of the reference coordinates.</dd>
931 <dd>The reference coordinates are scaled with the scaling matrix of the pressure coupling.</dd>
933 <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.
940 <h3>Simulated annealing<!--QuietIdx-->simulated annealing<!--EQuietIdx--></h3>
942 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!
944 <dt><b>annealing:</b></dt>
945 <dd>Type of annealing for each temperature group</dd>
946 <dd><dl compact></dd>
948 <dd>No simulated annealing - just couple to reference temperature value.</dd>
949 <dt><b>single</b></dt>
950 <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>
951 <dt><b>periodic</b></dt>
952 <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.
956 <dt><b>annealing-npoints:</b></dt>
957 <dd>A list with the number of annealing reference/control points used for
958 each temperature group. Use 0 for groups that are not annealed. The number of entries should equal the number of temperature groups.</dd>
960 <dt><b>annealing-time:</b></dt>
961 <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>
963 <dt><b>annealing-temp:</b></dt>
964 <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>
966 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>.
967 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!
972 <h3>Velocity generation</h3>
975 <dt><b>gen-vel:</b></dt>
978 <dd> Do not generate velocities. The velocities are set to zero
979 when there are no velocities in the input structure file.</dd>
981 <dd>Generate velocities in <tt>grompp</tt> according to a Maxwell distribution at
982 temperature <b>gen-temp</b> [K], with random seed <b>gen-seed</b>.
983 This is only meaningful with integrator <b><A HREF="#run">md</A></b>.</dd>
985 <dt><b>gen-temp: (300) [K]</b></dt>
986 <dd>temperature for Maxwell distribution</dd>
987 <dt><b>gen-seed: (173529) [integer]</b></dt>
988 <dd>used to initialize random generator for random velocities,
989 when <b>gen-seed</b> is set to -1, the seed is calculated from
990 the process ID number.
998 <dt><b>constraints<!--QuietIdx-->constraint algorithms<!--QuietEIdx-->:</b></dt>
1000 <dt><b>none</b></dt>
1001 <dd>No constraints except for those defined explicitly in the topology,
1002 i.e. bonds are represented by a harmonic (or other) potential
1003 or a Morse potential (depending on the setting of <b>morse</b>)
1004 and angles by a harmonic (or other) potential.
1005 <dt><b>h-bonds</b></dt>
1006 <dd>Convert the bonds with H-atoms to constraints.</dd>
1007 <dt><b>all-bonds</b></dt>
1008 <dd>Convert all bonds to constraints.</dd>
1009 <dt><b>h-angles</b></dt>
1010 <dd>Convert all bonds and additionally the angles that involve H-atoms
1011 to bond-constraints.</dd>
1012 <dt><b>all-angles</b></dt>
1013 <dd>Convert all bonds and angles to bond-constraints.</dd>
1016 <dt><b>constraint-algorithm:</b></dt>
1018 <dt><b><!--Idx-->LINCS<!--EIdx--></b></dt>
1019 <dd>LINear Constraint Solver.
1020 With domain decomposition the parallel version P-LINCS is used.
1021 The accuracy in set with
1022 <b>lincs-order</b>, which sets the number of matrices in the expansion
1023 for the matrix inversion.
1024 After the matrix inversion correction the algorithm does
1025 an iterative correction to compensate for lengthening due to rotation.
1026 The number of such iterations can be controlled with
1027 <b>lincs-iter</b>. The root mean square relative constraint deviation
1028 is printed to the log file every <b>nstlog</b> steps.
1029 If a bond rotates more than <b>lincs-warnangle</b> [degrees] in one step,
1030 a warning will be printed both to the log file and to <TT>stderr</TT>.
1031 LINCS should not be used with coupled angle constraints.
1033 <dt><b><!--Idx-->SHAKE<!--EIdx--></b></dt>
1034 <dd>SHAKE is slightly slower and less stable than LINCS, but does work with
1036 The relative tolerance is set with <b>shake-tol</b>, 0.0001 is a good value
1037 for ``normal'' MD. SHAKE does not support constraints between atoms
1038 on different nodes, thus it can not be used with domain decompositon
1039 when inter charge-group constraints are present.
1040 SHAKE can not be used with energy minimization.
1043 <dt><b>continuation:</b></dt>
1044 <dd>This option was formerly known as <tt>unconstrained-start</tt>.</dd>
1047 <dd>apply constraints to the start configuration and reset shells</dd>
1049 <dd>do not apply constraints to the start configuration
1050 and do not reset shells, useful for exact coninuation and reruns</dd>
1054 <dt><b>shake-tol: (0.0001)</b></dt>
1055 <dd>relative tolerance for SHAKE</dd>
1056 <dt><b>lincs-order: (4)</b></dt>
1057 <dd>Highest order in the expansion of the constraint coupling matrix.
1058 When constraints form triangles, an additional expansion of the same
1059 order is applied on top of the normal expansion only for the couplings
1060 within such triangles.
1061 For ``normal'' MD simulations an order of 4 usually suffices, 6 is
1062 needed for large time-steps with virtual sites or BD.
1063 For accurate energy minimization an order of 8 or more might be required.
1064 With domain decomposition, the cell size is limited by the distance
1065 spanned by <b>lincs-order</b>+1 constraints. When one wants to scale
1066 further than this limit, one can decrease <b>lincs-order</b> and increase
1067 <b>lincs-iter</b>, since the accuracy does not deteriorate
1068 when (1+<b>lincs-iter</b>)*<b>lincs-order</b> remains constant.</dd>
1069 <dt><b>lincs-iter: (1)</b></dt>
1070 <dd>Number of iterations to correct for rotational lengthening in LINCS.
1071 For normal runs a single step is sufficient, but for NVE
1072 runs where you want to conserve energy accurately or for accurate
1073 energy minimization you might want to increase it to 2.
1074 <dt><b>lincs-warnangle: </b>(30) [degrees]</dt>
1075 <dd>maximum angle that a bond can rotate before LINCS will complain</dd>
1077 <dt><b>morse:</b></dt>
1080 <dd>bonds are represented by a harmonic potential</dd>
1082 <dd>bonds are represented by a Morse potential</dd>
1086 <A NAME="egexcl"><br>
1088 <h3>Energy group <!--Idx-->exclusions<!--EIdx--></h3>
1090 <dt><b>energygrp-excl: </b></dt>
1091 <dd>Pairs of energy groups for which all non-bonded interactions are
1092 excluded. An example: if you have two energy groups <tt>Protein</tt>
1093 and <tt>SOL</tt>, specifying
1095 <tt>energygrp-excl = Protein Protein SOL SOL</tt>
1097 would give only the non-bonded interactions between the protein and the
1098 solvent. This is especially useful for speeding up energy calculations with
1099 <tt>mdrun -rerun</tt> and for excluding interactions within frozen groups.</dd>
1102 <A NAME="walls"><br>
1104 <h3>Walls<!--QuietIdx-->walls<!--EQuietIdx--></h3>
1106 <dt><b>nwall: 0</b></dt>
1107 <dd>When set to <b>1</b> there is a wall at <tt>z=0</tt>, when set to <b>2</b>
1108 there is also a wall at <tt>z=z-box</tt>. Walls can only be used with <b>pbc=xy</b>.
1109 When set to <b>2</b> pressure coupling and Ewald summation can be used
1110 (it is usually best to use semiisotropic pressure coupling with
1111 the <tt>x/y</tt> compressibility set to 0, as otherwise the surface area will change).
1112 Walls interact wit the rest of the system through an optional <tt>wall-atomtype</tt>.
1113 Energy groups <tt>wall0</tt> and <tt>wall1</tt> (for <b>nwall=2</b>) are
1114 added automatically to monitor the interaction of energy groups
1116 The <A HREF="#run">center of mass motion removal</A> will be turned
1117 off in the <tt>z</tt>-direction.</dd>
1118 <dt><b>wall-atomtype:</b></dt>
1119 <dd>the atom type name in the force field for each wall.
1120 By (for example) defining a special wall atom type in the topology with its
1121 own combination rules, this allows for independent tuning of the interaction
1122 of each atomtype with the walls.</dd>
1123 <dt><b>wall-type:</b></dt>
1126 <dd>LJ integrated over the volume behind the wall: 9-3 potential</dd>
1127 <dt><b>10-4</b></dt>
1128 <dd>LJ integrated over the wall surface: 10-4 potential</dd>
1129 <dt><b>12-6</b></dt>
1130 <dd>direct LJ potential with the z distance from the wall</dd>
1131 <dt><b>table</b></dt><dd>user defined potentials indexed with the z distance from the wall, the tables are read analogously to
1132 the <b><A HREF="#table">energygrp-table</A></b> option,
1133 where the first name is for a ``normal'' energy group and the second name
1134 is <tt>wall0</tt> or <tt>wall1</tt>,
1135 only the dispersion and repulsion columns are used</dd>
1137 <dt><b>wall-r-linpot: -1 (nm)</b></dt>
1138 <dd>Below this distance from the wall the potential is continued
1139 linearly and thus the force is constant. Setting this option to
1140 a postive value is especially useful for equilibration when some atoms
1142 When the value is ≤0 (<0 for <b>wall-type=table</b>),
1143 a fatal error is generated when atoms are beyond a wall.
1145 <dt><b>wall-density: [nm<sup>-3</sup>/nm<sup>-2</sup>]</b></dt>
1146 <dd>the number density of the atoms for each wall for wall types
1147 <b>9-3</b> and <b>10-4</b>
1148 <dt><b>wall-ewald-zfac: 3</b></dt>
1149 <dd>The scaling factor for the third box vector for Ewald summation only,
1151 Ewald summation can only be used with <b>nwall=2</b>, where one
1152 should use <b><A HREF="#ewald">ewald-geometry</A><tt>=3dc</tt></b>.
1153 The empty layer in the box serves to decrease the unphysical Coulomb
1154 interaction between periodic images.
1159 <h3>COM <!--Idx-->pulling<!--EIdx--></h3>
1161 <dt><b>pull:</b></dt>
1164 <dd>No center of mass pulling.
1165 All the following pull options will be ignored
1166 (and if present in the <tt>.mdp</tt> file, they unfortunately generate warnings)</dd>
1167 <dt><b>umbrella</b></dt>
1168 <dd>Center of mass pulling using an umbrella potential
1169 between the reference group and one or more groups.</dd>
1170 <dt><b>constraint</b></dt>
1171 <dd>Center of mass pulling using a constraint
1172 between the reference group and one or more groups.
1173 The setup is identical to the option <b>umbrella</b>, except for the fact
1174 that a rigid constraint is applied instead of a harmonic potential.</dd>
1175 <dt><b>constant-force</b></dt>
1176 <dd>Center of mass pulling using a linear potential and therefore
1177 a constant force. For this option there is no reference position
1178 and therefore the parameters <b>pull-init</b> and <b>pull-rate</b>
1181 <dt><b>pull-geometry:</b></dt>
1183 <dt><b>distance</b></dt>
1184 <dd>Pull along the vector connecting the two groups.
1185 Components can be selected with <b>pull-dim</b>.</dd>
1186 <dt><b>direction</b></dt>
1187 <dd>Pull in the direction of <b>pull-vec</b>.</dd>
1188 <dt><b>direction-periodic</b></dt>
1189 <dd>As <b>direction</b>, but allows the distance to be larger than
1190 half the box size. With this geometry the box should not be dynamic
1191 (e.g. no pressure scaling) in the pull dimensions and the pull force
1192 is not added to virial.</dd>
1193 <dt><b>cylinder</b></dt>
1194 <dd>Designed for pulling with respect to a layer where the reference COM
1195 is given by a local cylindrical part of the reference group.
1196 The pulling is in the direction of <b>pull-vec</b>.
1197 From the reference group a cylinder is selected around the axis going
1198 through the pull group with direction <b>pull-vec</b> using two radii.
1199 The radius <b>pull-r1</b> gives the radius within which all
1200 the relative weights are one, between <b>pull-r1</b> and
1201 <b>pull-r0</b> the weights are switched to zero. Mass weighting is also used.
1202 Note that the radii should be smaller than half the box size.
1203 For tilted cylinders they should be even smaller than half the box size
1204 since the distance of an atom in the reference group
1205 from the COM of the pull group has both a radial and an axial component.
1206 <dt><b>position</b></dt>
1207 <dd>Pull to the position of the reference group plus
1208 <b>pull-init</b> + time*<b>pull-rate</b>*<b>pull-vec</b>.</dd>
1210 <dt><b>pull-dim: (Y Y Y)</b></dt>
1211 <dd>the distance components to be used with geometry <b>distance</b>
1212 and <b>position</b>, and also sets which components are printed
1213 to the output files</dd>
1214 <dt><b>pull-r1: (1) [nm]</b></dt>
1215 <dd>the inner radius of the cylinder for geometry <b>cylinder</b></dd>
1216 <dt><b>pull-r0: (1) [nm]</b></dt>
1217 <dd>the outer radius of the cylinder for geometry <b>cylinder</b></dd>
1218 <dt><b>pull-constr-tol: (1e-6)</b></dt>
1219 <dd>the relative constraint tolerance for constraint pulling</dd>
1220 <dt><b>pull-start:</b></dt>
1223 <dd>do not modify <b>pull-init</b>
1225 <dd>add the COM distance of the starting conformation to <b>pull-init</b></dd>
1227 <dt><b>pull-nstxout: (10)</b></dt>
1228 <dd>frequency for writing out the COMs of all the pull group</dd>
1229 <dt><b>pull-nstfout: (1)</b></dt>
1230 <dd>frequency for writing out the force of all the pulled group</dd>
1231 <dt><b>pull-ngroups: (1)</b></dt>
1232 <dd>The number of pull groups, not including the reference group.
1233 If there is only one group, there is no difference in treatment
1234 of the reference and pulled group (except with the cylinder geometry).
1235 Below only the pull options for the reference group (ending on 0)
1236 and the first group (ending on 1) are given,
1237 further groups work analogously, but with the number 1 replaced
1238 by the group number.</dd>
1239 <dt><b>pull-group0: </b></dt>
1240 <dd>The name of the reference group. When this is empty an absolute reference
1241 of (0,0,0) is used. With an absolute reference the system is no longer
1242 translation invariant and one should think about what to do with
1243 the <A HREF="#run">center of mass motion</A>.</dd>
1244 <dt><b>pull-weights0: </b></dt>
1245 <dd>see <b>pull-weights1</b></dd>
1246 <dt><b>pull-pbcatom0: (0)</b></dt>
1247 <dd>see <b>pull-pbcatom1</b></dd>
1248 <dt><b>pull-group1: </b></dt>
1249 <dd>The name of the pull group.</dd>
1250 <dt><b>pull-weights1: </b></dt>
1251 <dd>Optional relative weights which are multiplied with the masses of the atoms
1252 to give the total weight for the COM. The number should be 0, meaning all 1,
1253 or the number of atoms in the pull group.</dd>
1254 <dt><b>pull-pbcatom1: (0)</b></dt>
1255 <dd>The reference atom for the treatment of periodic boundary conditions
1257 (this has no effect on the treatment of the pbc between groups).
1258 This option is only important when the diameter of the pull group
1259 is larger than half the shortest box vector.
1260 For determining the COM, all atoms in the group are put at their periodic image
1261 which is closest to <b>pull-pbcatom1</b>.
1262 A value of 0 means that the middle atom (number wise) is used.
1263 This parameter is not used with geometry <b>cylinder</b>.
1264 A value of -1 turns on cosine weighting, which is useful for a group
1265 of molecules in a periodic system, e.g. a water slab (see Engin et al.
1266 J. Chem. Phys. B 2010).</dd>
1267 <dt><b>pull-vec1: (0.0 0.0 0.0)</b></dt>
1268 <dd>The pull direction. <tt>grompp</tt> normalizes the vector.</dd>
1269 <dt><b>pull-init1: (0.0) / (0.0 0.0 0.0) [nm]</b></dt>
1270 <dd>The reference distance at t=0. This is a single value,
1271 except for geometry <b>position</b> which uses a vector.</dd>
1272 <dt><b>pull-rate1: (0) [nm/ps]</b></dt>
1273 <dd>The rate of change of the reference position.</dd>
1274 <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>
1275 <dd>The force constant. For umbrella pulling this is the harmonic force
1276 constant in [kJ mol<sup>-1</sup> nm<sup>-2</sup>]. For constant force pulling
1277 this is the force constant of the linear potential, and thus minus (!)
1278 the constant force in [kJ mol<sup>-1</sup> nm<sup>-1</sup>].</dd>
1279 <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>
1280 <dd>As <b>pull-k1</b>, but for state B. This is only used when
1281 <A HREF="#free"><b>free-energy</b></A> is turned on.
1282 The force constant is then (1 - lambda)*<b>pull-k1</b> + lambda*<b>pull-kB1</b>.
1287 <h3><!--Idx-->NMR refinement<!--EIdx--></h3>
1289 <dt><b>disre:</b></dt>
1292 <dd>ignore <!--Idx-->distance restraint<!--EIdx--> information in topology file</dd>
1293 <dt><b>simple</b></dt>
1294 <dd>simple (per-molecule) distance restraints.
1295 <dt><b>ensemble</b></dt>
1296 <dd>distance restraints over an ensemble of molecules in one
1297 simulation box. Normally, one would perform ensemble averaging over
1298 multiple subsystems, each in a separate box, using <tt>mdrun -multi</tt>;s
1299 upply <tt>topol0.tpr</tt>, <tt>topol1.tpr</tt>, ... with different
1300 coordinates and/or velocities.
1301 The environment variable <tt>GMX_DISRE_ENSEMBLE_SIZE</tt> sets the number
1302 of systems within each ensemble (usually equal to the <tt>mdrun -multi</tt> value).</dd>
1305 <dt><b>disre-weighting:</b></dt>
1307 <dt><b>equal</b> (default)</dt>
1308 <dd>divide the restraint force equally over all atom pairs in the restraint</dd>
1309 <dt><b>conservative</b></dt>
1310 <dd>the forces are the derivative of the restraint potential,
1311 this results in an r<sup>-7</sup> weighting of the atom pairs.
1312 The forces are conservative when <tt>disre-tau</tt> is zero.</dd>
1314 <dt><b>disre-mixed:</b></dt>
1317 <dd>the violation used in the calculation of the restraint force is the
1318 time-averaged violation </dd>
1320 <dd>the violation used in the calculation of the restraint force is the
1321 square root of the product of the time-averaged violation and the instantaneous violation</dd>
1324 <dt><b>disre-fc: (1000) [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
1325 <dd>force constant for distance restraints, which is multiplied by a
1326 (possibly) different factor for each restraint given in the <tt>fac</tt>
1327 column of the interaction in the topology file.</dd>
1329 <dt><b>disre-tau: (0) [ps]</b></dt>
1330 <dd>time constant for distance restraints running average. A value of zero turns off time averaging.</dd>
1332 <dt><b>nstdisreout: (100) [steps]</b></dt>
1333 <dd>period between steps when the running time-averaged and instantaneous distances
1334 of all atom pairs involved in restraints are written to the energy file
1335 (can make the energy file very large)</dd>
1338 <dt><b>orire:</b></dt>
1341 <dd>ignore <!--Idx-->orientation restraint<!--EIdx--> information in topology file</dd>
1343 <dd>use orientation restraints, ensemble averaging can be performed
1344 with <tt>mdrun -multi</tt></dd>
1346 <dt><b>orire-fc: (0) [kJ mol]</b></dt>
1347 <dd>force constant for orientation restraints, which is multiplied by a
1348 (possibly) different weight factor for each restraint, can be set to zero to
1349 obtain the orientations from a free simulation</dd>
1350 <dt><b>orire-tau: (0) [ps]</b></dt>
1351 <dd>time constant for orientation restraints running average. A value of zero turns off time averaging.</dd>
1352 <dt><b>orire-fitgrp: </b></dt>
1353 <dd>fit group for orientation restraining. This group of atoms is used
1354 to determine the rotation <b>R</b> of the system with respect to the
1355 reference orientation. The reference orientation is the starting
1356 conformation of the first subsystem. For a protein, backbone is a reasonable
1358 <dt><b>nstorireout: (100) [steps]</b></dt>
1359 <dd>period between steps when the running time-averaged and instantaneous orientations
1360 for all restraints, and the molecular order tensor are written to the energy file
1361 (can make the energy file very large)</dd>
1366 <h3>Free energy calculations<!--QuietIdx-->free energy calculations<!--EQuietIdx--></h3>
1369 <dt><b>free-energy:</b></dt>
1372 <dd>Only use topology A.</dd>
1374 <dd>Interpolate between topology A (lambda=0) to topology B (lambda=1)
1375 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
1376 the energy file and/or to <tt>dhdl.xvg</tt>, where they can be processed by, for example <tt>g_bar</tt>.
1377 The potentials, bond-lengths and angles are interpolated linearly as
1378 described in the manual. When <b>sc-alpha</b> is larger than zero, soft-core
1379 potentials are used for the LJ and Coulomb interactions.</dd>
1381 <dt><b>init-lambda: (0)</b></dt>
1382 <dd>starting value for lambda</dd>
1383 <dt><b>delta-lambda: (0)</b></dt>
1384 <dd>increment per time step for lambda</dd>
1385 <dt><b>foreign-lambda: ()</b></dt>
1386 <dd>Zero, one or more lambda values for which Delta H values will
1387 be determined and written to dhdl.xvg every <b>nstdhdl</b> steps.
1388 Free energy differences between different lambda values can then
1389 be determined with <tt>g_bar</tt>.</dd>
1390 <dt><b>dhdl-derivatives: (yes)</b></dt>
1391 <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>
1392 <dt><b>sc-alpha: (0)</b></dt>
1393 <dd>the soft-core parameter, a value of 0 results in linear interpolation of
1394 the LJ and Coulomb interactions</dd>
1395 <dt><b>sc-power: (0)</b></dt>
1396 <dd>the power for lambda in the soft-core function,
1397 only the values 1 and 2 are supported</dd>
1398 <dt><b>sc-sigma: (0.3) [nm]</b></dt>
1399 <dd>the soft-core sigma for particles which have a C6 or C12 parameter equal
1400 to zero or a sigma smaller than <b>sc-sigma</b></dd>
1401 <dt><b>couple-moltype:</b></dt>
1402 <dd>Here one can supply a molecule type (as defined in the topology)
1403 for calculating solvation or coupling free energies.
1404 There is a special option <b>system</b> that couples all molecule types
1405 in the system. This can be useful for equilibrating a system
1406 starting from (nearly) random coordinates.
1407 <b>free-energy</b> has to be turned on.
1408 The Van der Waals interactions and/or charges in this molecule type can be
1409 turned on or off between lambda=0 and lambda=1, depending on the settings
1410 of <b>couple-lambda0</b> and <b>couple-lambda1</b>. If you want to decouple
1411 one of several copies of a molecule, you need to copy and rename
1412 the molecule definition in the topology.</dd>
1413 <dt><b>couple-lambda0:</b></dt>
1415 <dt><b>vdw-q</b></dt>
1416 <dd>all interactions are on at lambda=0
1418 <dd>the charges are zero (no Coulomb interactions) at lambda=0
1420 <dd>the Van der Waals interactions are turned at lambda=0; soft-core interactions will be required to avoid singularities
1421 <dt><b>none</b></dt>
1422 <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
1424 <dt><b>couple-lambda1:</b></dt>
1425 <dd> analogous to <b>couple-lambda1</b>, but for lambda=1
1426 <dt><b>couple-intramol:</b></dt>
1429 <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.
1431 <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.
1433 <dt><b>nstdhdl: (10)</b></dt>
1434 <dd>the frequency for writing dH/dlambda and possibly Delta H to dhdl.xvg,
1435 0 means no ouput, should be a multiple of <b>nstcalcenergy</b></dd>
1436 <dt><b>separate-dhdl-file: (yes)</b></dt>
1439 <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>
1441 <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>
1443 <dt><b>dh-hist-size: (0)</b></dt>
1444 <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>
1445 <dt><b>dh-hist-spacing (0.1)</b></dt>
1446 <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>
1452 <h3>Non-equilibrium MD<!--QuietIdx-->non-equilibrium MD<!--EQuietIdx--></h3>
1455 <dt><b>acc-grps: </b></dt>
1456 <dd>groups for constant acceleration (e.g.: <tt>Protein Sol</tt>)
1457 all atoms in groups Protein and Sol will experience constant acceleration
1458 as specified in the <b>accelerate</b> line</dd>
1459 <dt><b>accelerate: (0) [nm ps<sup>-2</sup>]</b></dt>
1460 <dd>acceleration for <b>acc-grps</b>; x, y and z for each group
1461 (e.g. <tt>0.1 0.0 0.0 -0.1 0.0 0.0</tt> means that first group has constant
1462 acceleration of 0.1 nm ps<sup>-2</sup> in X direction, second group the
1464 <dt><b>freezegrps: </b></dt>
1465 <dd>Groups that are to be frozen (i.e. their X, Y, and/or Z position will
1466 not be updated; e.g. <tt>Lipid SOL</tt>). <b>freezedim</b> specifies for
1467 which dimension the freezing applies.
1468 To avoid spurious contibrutions to the virial and pressure due to large
1469 forces between completely frozen atoms you need to use
1470 <A HREF="#egexcl">energy group exclusions</A>, this also saves computing time.
1471 Note that coordinates of frozen atoms are not scaled by pressure-coupling
1473 <dt><b>freezedim: </b></dt>
1474 <dd>dimensions for which groups in <b>freezegrps</b> should be frozen,
1475 specify <tt>Y</tt> or <tt>N</tt> for X, Y and Z and for each group
1476 (e.g. <tt>Y Y N N N N</tt> means that particles in the first group
1477 can move only in Z direction. The particles in the second group can
1478 move in any direction).</dd>
1479 <dt><b>cos-acceleration: (0) [nm ps<sup>-2</sup>]</b></dt>
1480 <dd>the amplitude of the acceleration profile for calculating the
1481 <!--Idx-->viscosity<!--EIdx-->.
1482 The acceleration is in the X-direction and the magnitude is
1483 <b>cos-acceleration</b> cos(2 pi z/boxheight).
1484 Two terms are added to the energy file:
1485 the amplitude of the velocity profile and 1/viscosity.</dd>
1486 <dt><b><!--Idx-->deform<!--EIdx-->: (0 0 0 0 0 0) [nm ps<sup>-1</sup>]</b></dt>
1487 <dd>The velocities of deformation for the box elements:
1488 a(x) b(y) c(z) b(x) c(x) c(y). Each step the box elements
1489 for which <b>deform</b> is non-zero are calculated as:
1490 box(ts)+(t-ts)*deform, off-diagonal elements are corrected
1491 for periodicity. The coordinates are transformed accordingly.
1492 Frozen degrees of freedom are (purposely) also transformed.
1493 The time ts is set to t at the first step and at steps at which
1494 x and v are written to trajectory to ensure exact restarts.
1495 Deformation can be used together with semiisotropic or anisotropic
1496 pressure coupling when the appropriate compressibilities are set to zero.
1497 The diagonal elements can be used to <!--Idx-->strain<!--EIdx--> a solid.
1498 The off-diagonal elements can be used to <!--Idx-->shear<!--EIdx--> a solid
1504 <h3>Electric fields<!--QuietIdx-->electric field<!--EQuietIdx--></h3>
1507 <dt><b>E-x ; E-y ; E-z:</b></dt>
1508 <dd>If you want to use an electric field in a direction, enter 3 numbers
1509 after the appropriate <b>E-*</b>, the first number: the number of cosines,
1510 only 1 is implemented (with frequency 0) so enter 1,
1511 the second number: the strength of the electric field in
1512 <b>V nm<sup>-1</sup></b>,
1513 the third number: the phase of the cosine, you can enter any number here
1514 since a cosine of frequency zero has no phase.</dd>
1515 <dt><b>E-xt; E-yt; E-zt: </b></dt>
1516 <dd>not implemented yet</dd>
1522 <h3>Mixed quantum/classical molecular dynamics<!--QuietIdx>QM/MM<!--EQuietIdx--></h3>
1525 <dt><b>QMMM:</b></dt>
1526 <dd><dl compact="compact">
1530 <dd>Do a QM/MM simulation. Several groups can be described at
1531 different QM levels separately. These are specified in
1532 the <b>QMMM-grps</b> field separated by spaces. The level of <i>ab
1533 initio</i> theory at which the groups are described is specified
1534 by <b>QMmethod</b> and <b>QMbasis</b> Fields. Describing the
1535 groups at different levels of theory is only possible with the ONIOM
1536 QM/MM scheme, specified by <b>QMMMscheme</b>.</dd>
1539 <dt><b>QMMM-grps:</b></dt>
1540 <dd>groups to be descibed at the QM level</dd>
1542 <dt><b>QMMMscheme:</b></dt>
1543 <dd><dl compact="compact">
1544 <dt><b>normal</b></dt>
1545 <dd>normal QM/MM. There can only be one <b>QMMM-grps</b> that is modelled
1546 at the <b>QMmethod</b> and <b>QMbasis</b> level of <i>ab initio</i>
1547 theory. The rest of the system is described at the MM level. The QM
1548 and MM subsystems interact as follows: MM point charges are included
1549 in the QM one-electron hamiltonian and all Lennard-Jones interactions
1550 are described at the MM level.</dd>
1551 <dt><b>ONIOM</b></dt>
1552 <dd>The interaction between the subsystem is described using the ONIOM
1553 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
1554 (<b>QMmethod</b> and <b>QMbasis</b>).
1557 <dt><b>QMmethod: (RHF)</b></dt>
1558 <dd>Method used to compute the energy and gradients on the QM
1559 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
1560 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
1561 included in the active space is specified by <b>CASelectrons</b>
1562 and <b>CASorbitals</b>. </dd>
1564 <dt><b>QMbasis: (STO-3G)</b></dt>
1565 <dd>Basis set used to expand the electronic wavefuntion. Only Gaussian
1566 basis sets are currently available, <i>i.e.</i> STO-3G, 3-21G, 3-21G*,
1567 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*, and 6-311G.</dd>
1569 <dt><b>QMcharge: (0) [integer]</b></dt>
1570 <dd>The total charge in <tt>e</tt> of the <b>QMMM-grps</b>. In case
1571 there are more than one <b>QMMM-grps</b>, the total charge of each
1572 ONIOM layer needs to be specified separately.</dd>
1574 <dt><b>QMmult: (1) [integer]</b></dt>
1575 <dd>The multiplicity of the <b>QMMM-grps</b>. In case there are more
1576 than one <b>QMMM-grps</b>, the multiplicity of each ONIOM layer needs
1577 to be specified separately.</dd>
1579 <dt><b>CASorbitals: (0) [integer]</b></dt>
1580 <dd>The number of orbitals to be included in the active space when
1581 doing a CASSCF computation.</dd>
1583 <dt><b>CASelectrons: (0) [integer]</b></dt>
1584 <dd>The number of electrons to be included in the active space when
1585 doing a CASSCF computation.</dd>
1588 <dd><dl compact="compact">
1590 <dd>No surface hopping. The system is always in the electronic
1593 <dd>Do a QM/MM MD simulation on the excited state-potential energy
1594 surface and enforce a <i>diabatic</i> hop to the ground-state when the
1595 system hits the conical intersection hyperline in the course the
1596 simulation. This option only works in combination with the CASSCF
1603 <h3>Implicit solvent</h3>
1606 <dt><b>implicit-solvent:</b></dt>
1607 <dd><dl compact="compact">
1609 <dd>No implicit solvent</dd>
1610 <dt><b>GBSA</b></dt>
1611 <dd>Do a simulation with implicit solvent using the Generalized Born formalism.
1612 Three different methods for calculating the Born radii are available, Still, HCT and
1613 OBC. These are specified with the <b>gb-algorithm</b> field. The non-polar solvation
1614 is specified with the <b>sa-algorithm</b> field.</dd>
1617 <dt><b>gb-algorithm:</b></dt>
1618 <dd><dl compact="compact">
1619 <dt><b>Still</b></dt>
1620 <dd>Use the Still method to calculate the Born radii</dd>
1622 <dd>Use the Hawkins-Cramer-Truhlar method to calculate the Born radii</dd>
1624 <dd>Use the Onufriev-Bashford-Case method to calculate the Born radii</dd>
1627 <dt><b>nstgbradii: (1) [steps]</b></dt>
1628 <dd>Frequency to (re)-calculate the Born radii. For most practial purposes,
1629 setting a value larger than 1 violates energy conservation and leads to
1630 unstable trajectories.</dd>
1632 <dt><b>rgbradii: (1.0) [nm]</b></dt>
1633 <dd>Cut-off for the calculation of the Born radii. Currently must be equal to rlist</dd>
1635 <dt><b>gb-epsilon-solvent: (80)</b></dt>
1636 <dd>Dielectric constant for the implicit solvent</dd>
1638 <dt><b>gb-saltconc: (0) [M]</b></dt>
1639 <dd>Salt concentration for implicit solvent models, currently not used</dd>
1641 <dt><b>gb-obc-alpha (1); gb-obc-beta (0.8); gb-obc-gamma (4.85);</b></dt>
1642 <dd>Scale factors for the OBC model. Default values are OBC(II).
1643 Values for OBC(I) are 0.8, 0 and 2.91 respectively</dd>
1645 <dt><b>gb-dielectric-offset: (0.009) [nm]</b></dt>
1646 <dd>Distance for the di-electric offset when calculating the Born radii. This is
1647 the offset between the center of each atom the center of the polarization energy
1648 for the corresponding atom</dd>
1650 <dt><b>sa-algorithm</b></dt>
1651 <dd><dl compact="compact">
1652 <dt><b>Ace-approximation</b></dt>
1653 <dd>Use an Ace-type approximation (default)</dd>
1654 <dt><b>None</b></dt>
1655 <dd>No non-polar solvation calculation done. For GBSA only the polar part gets
1659 <dt><b>sa-surface-tension: [kJ mol<sup>-1</sup> nm<sup>-2</sup>]</b></dt>
1660 <dd>Default value for surface tension with SA algorithms. The default value is -1;
1661 Note that if this default value is not changed
1662 it will be overridden by <tt>grompp</tt> using values that are specific for the choice
1663 of radii algorithm (0.0049 kcal/mol/Angstrom<sup>2</sup> for Still, 0.0054 kcal/mol/Angstrom<sup>2</sup>
1666 Setting it to 0 will while using an sa-algorithm other than None means
1667 no non-polar calculations are done.
1671 <A NAME="adress"><br>
1673 <h3>Adaptive Resolution Simulation</h3>
1676 <dt><b>adress: (no)</b></dt>
1677 <dd>Decide whether the AdResS feature is turned on.</dd>
1678 <dt><b>adress-type: (Off)</b></dt>
1681 <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>
1682 <dt><b>Constant</b></dt>
1683 <dd>Do an AdResS simulation with a constant weight, <b>adress-const-wf</b> defines the value of the weight</dd>
1684 <dt><b>XSplit</b></dt>
1685 <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>
1686 <dt><b>Sphere</b></dt>
1687 <dd>Do an AdResS simulation with spherical explicit zone.</dd>
1689 <dt><b>adress-const-wf: (1)</b></dt>
1690 <dd>Provides the weight for a constant weight simulation (<b>adress-type</b>=Constant)</dd>
1691 <dt><b>adress-ex-width: (0)</b></dt>
1692 <dd>Width of the explicit zone, measured from <b>adress-reference-coords</b>.</dd>
1693 <dt><b>adress-hy-width: (0)</b></dt>
1694 <dd>Width of the hybrid zone.</dd>
1695 <dt><b>adress-reference-coords: (0,0,0)</b></dt>
1696 <dd>Position of the center of the explicit zone. Periodic boundary conditions apply for measuring the distance from it.</dd>
1697 <dt><b>adress-cg-grp-names</b></dt>
1698 <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>
1699 <dt><b>adress-site: (COM)</b>The mapping point from which the weight is calculated.</dt>
1702 <dd>The weight is calculated from the center of mass of each charge group.</dd>
1704 <dd>The weight is calculated from the center of geometry of each charge group.</dd>
1705 <dt><b>Atom</b></dt>
1706 <dd>The weight is calculated from the position of 1st atom of each charge group.</dd>
1707 <dt><b>AtomPerAtom</b></dt>
1708 <dd>The weight is calculated from the position of each individual atom.</dd>
1710 <dt><b>adress-interface-correction: (Off)</b></dt>
1713 <dd>Do not a apply any interface correction.</dd>
1714 <dt><b>thermoforce</b></dt>
1715 <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>
1717 <dt><b>adress-tf-grp-names</b></dt>
1718 <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>
1719 <dt><b>adress-ex-forcecap: (0)</b></dt>
1720 <dd>Cap the force in the hybrid region, useful for big molecules. 0 disables force capping.</dd>
1725 <h3>User defined thingies</h3>
1728 <dt><b>user1-grps; user2-grps: </b></dt>
1729 <dt><b>userint1 (0); userint2 (0); userint3 (0); userint4 (0)</b></dt>
1730 <dt><b>userreal1 (0); userreal2 (0); userreal3 (0); userreal4 (0)</b></dt>
1731 <dd>These you can use if you modify code. You can pass integers and
1732 reals to your subroutine. Check the inputrec definition in
1733 <tt>src/include/types/inputrec.h</tt></dd>
1744 <A HREF="#neq">acc-grps</A><br>
1745 <A HREF="#neq">accelerate</A><br>
1746 <A HREF="#sa">annealing</A><br>
1747 <A HREF="#sa">annealing-npoints</A><br>
1748 <A HREF="#sa">annealing-time</A><br>
1749 <A HREF="#sa">annealing-temp</A><br>
1750 <A HREF="#ld">bd-fric</A><br>
1751 <A HREF="#vdw">bDispCorr</A><br>
1752 <A HREF="#run">comm-mode</A><br>
1753 <A HREF="#run">comm-grps</A><br>
1754 <A HREF="#pc">compressibility</A><br>
1755 <A HREF="#bond">constraint-algorithm</A><br>
1756 <A HREF="#bond">constraints</A><br>
1757 <A HREF="#neq">cos-acceleration</A><br>
1758 <A HREF="#el">coulombtype</A><br>
1759 <A HREF="#free">couple-intramol</A><br>
1760 <A HREF="#free">couple-lambda0</A><br>
1761 <A HREF="#free">couple-lambda1</A><br>
1762 <A HREF="#free">couple-moltype</A><br>
1763 <A HREF="#pp">define</A><br>
1764 <A HREF="#neq">deform</A><br>
1765 <A HREF="#free">delta-lambda</A><br>
1766 <A HREF="#nmr">disre</A><br>
1767 <A HREF="#nmr">disre-weighting</A><br>
1768 <A HREF="#nmr">disre-mixed</A><br>
1769 <A HREF="#nmr">disre-fc</A><br>
1770 <A HREF="#nmr">disre-tau</A><br>
1771 <A HREF="#run">dt</A><br>
1772 <A HREF="#em">emstep</A><br>
1773 <A HREF="#em">emtol</A><br>
1774 <A HREF="#egexcl">energygrp-excl</A><br>
1775 <A HREF="#table">energygrp-table</A><br>
1776 <A HREF="#out">energygrps</A><br>
1777 <A HREF="#el2">epsilon-r</A><br>
1778 <A HREF="#el2">epsilon-rf</A><br>
1779 <A HREF="#ewald">ewald-rtol</A><br>
1780 <A HREF="#ewald">ewald-geometry</A><br>
1781 <A HREF="#ewald">epsilon-surface</A><br>
1782 <A HREF="#ef">E-x</A><br>
1783 <A HREF="#ef">E-xt</A><br>
1784 <A HREF="#ef">E-y</A><br>
1785 <A HREF="#ef">E-yt</A><br>
1786 <A HREF="#ef">E-z</A><br>
1787 <A HREF="#ef">E-zt </A><br>
1788 <A HREF="#xmdrun">fcstep</A><br>
1789 <A HREF="#ewald">fourier-nx</A><br>
1790 <A HREF="#ewald">fourier-ny</A><br>
1791 <A HREF="#ewald">fourier-nz</A><br>
1792 <A HREF="#ewald">fourierspacing</A><br>
1793 <A HREF="#free">free-energy</A><br>
1794 <A HREF="#neq">freezedim </A><br>
1795 <A HREF="#neq">freezegrps</A><br>
1796 <A HREF="#vel">gen-seed</A><br>
1797 <A HREF="#vel">gen-temp</A><br>
1798 <A HREF="#vel">gen-vel</A><br>
1799 <A HREF="#pp">include</A><br>
1800 <A HREF="#free">init-lambda</A><br>
1801 <A HREF="#run">init-step</A><br>
1802 <A HREF="#run">integrator</A><br>
1803 <A HREF="#ld">ld-seed</A><br>
1804 <A HREF="#bond2">lincs-iter</A><br>
1805 <A HREF="#bond2">lincs-order</A><br>
1806 <A HREF="#bond2">lincs-warnangle</A><br>
1807 <A HREF="#bond2">morse</A><br>
1808 <A HREF="#em">nbfgscorr</A><br>
1809 <A HREF="#xmdrun">niter</A><br>
1810 <A HREF="#tc">nh-chain-length</A><br>
1811 <A HREF="#em">nstcgsteep</A><br>
1812 <A HREF="#out">nstcalcenergy</A><br>
1813 <A HREF="#run">nstcomm</A><br>
1814 <A HREF="#nmr">nstdisreout</A><br>
1815 <A HREF="#out">nstenergy</A><br>
1816 <A HREF="#run">nsteps</A><br>
1817 <A HREF="#out">nstfout</A><br>
1818 <A HREF="#nl">nstlist</A><br>
1819 <A HREF="#out">nstlog</A><br>
1820 <A HREF="#pc">nstpcouple</A><br>
1821 <A HREF="#tc">nsttcouple</A><br>
1822 <A HREF="#out">nstvout</A><br>
1823 <A HREF="#out">nstxout</A><br>
1824 <A HREF="#out">nstxtcout</A><br>
1825 <A HREF="#nl">ns-type</A><br>
1826 <A HREF="#wall">nwall</A><br>
1827 <A HREF="#ewald">optimize-fft</A><br>
1828 <A HREF="#nmr2">orire</A><br>
1829 <A HREF="#nmr2">orire-fc</A><br>
1830 <A HREF="#nmr2">orire-tau</A><br>
1831 <A HREF="#nmr2">orire-fitgrp</A><br>
1832 <A HREF="#nmr2">nstorireout</A><br>
1833 <A HREF="#nl">pbc</A><br>
1834 <A HREF="#pc">pcoupl</A><br>
1835 <A HREF="#pc">pcoupltype</A><br>
1836 <A HREF="#nl">periodic-molecules</A><br>
1837 <A HREF="#ewald">pme-order</A><br>
1838 <A HREF="#pull">pull</A><br>
1839 <A HREF="#pc">refcoord-scaling</A><br>
1840 <A HREF="#pc">ref-p</A><br>
1841 <A HREF="#tc">ref-t</A><br>
1842 <A HREF="#el2">rcoulomb-switch</A><br>
1843 <A HREF="#el2">rcoulomb</A><br>
1844 <A HREF="#nl">rlist</A><br>
1845 <A HREF="#nl">rlistlong</A><br>
1846 <A HREF="#tpi">rtpi</A><br>
1847 <A HREF="#vdw">rvdw-switch</A><br>
1848 <A HREF="#vdw">rvdw</A><br>
1849 <A HREF="#free">sc-alpha</A><br>
1850 <A HREF="#free">sc-power</A><br>
1851 <A HREF="#free">sc-sigma</A><br>
1852 <A HREF="#bond2">shake-tol</A><br>
1853 <A HREF="#table">table-extension</A><br>
1854 <A HREF="#pc">tau-p</A><br>
1855 <A HREF="#tc">tau-t</A><br>
1856 <A HREF="#tc">tc-grps</A><br>
1857 <A HREF="#tc">tcoupl</A><br>
1858 <A HREF="#run">tinit</A><br>
1859 <A HREF="#bond">continuation</A><br>
1860 <A HREF="#user">user1-grps</A><br>
1861 <A HREF="#user">user2-grps</A><br>
1862 <A HREF="#user">userint1</A><br>
1863 <A HREF="#user">userint2</A><br>
1864 <A HREF="#user">userint3</A><br>
1865 <A HREF="#user">userint4</A><br>
1866 <A HREF="#user">userreal1</A><br>
1867 <A HREF="#user">userreal2</A><br>
1868 <A HREF="#user">userreal3</A><br>
1869 <A HREF="#user">userreal4</A><br>
1870 <A HREF="#el">vdwtype</A><br>
1871 <A HREF="#out">xtc-grps</A><br>
1872 <A HREF="#out">xtc-precision</A><br>
1873 <A HREF="#sa">zero-temp-time</A><br>
1874 <A HREF="#walls">wall-atomtype</A><br>
1875 <A HREF="#walls">wall-density</A><br>
1876 <A HREF="#walls">wall-ewald-zfac</A><br>
1877 <A HREF="#walls">wall-r-linpot</A><br>
1878 <A HREF="#walls">wall-type</A><br>
1883 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
biod.pnpi.spb.ru / alexxy / gromacs.git / blob