1 .TH mdrun 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
3 mdrun - performs a simulation, do a normal mode analysis or an energy minimization
8 .BI "\-s" " topol.tpr "
10 .BI "\-x" " traj.xtc "
11 .BI "\-cpi" " state.cpt "
12 .BI "\-cpo" " state.cpt "
13 .BI "\-c" " confout.gro "
14 .BI "\-e" " ener.edr "
16 .BI "\-dhdl" " dhdl.xvg "
17 .BI "\-field" " field.xvg "
18 .BI "\-table" " table.xvg "
19 .BI "\-tablep" " tablep.xvg "
20 .BI "\-tableb" " table.xvg "
21 .BI "\-rerun" " rerun.xtc "
22 .BI "\-tpi" " tpi.xvg "
23 .BI "\-tpid" " tpidist.xvg "
24 .BI "\-ei" " sam.edi "
25 .BI "\-eo" " sam.edo "
26 .BI "\-j" " wham.gct "
27 .BI "\-jo" " bam.gct "
28 .BI "\-ffout" " gct.xvg "
29 .BI "\-devout" " deviatie.xvg "
30 .BI "\-runav" " runaver.xvg "
31 .BI "\-px" " pullx.xvg "
32 .BI "\-pf" " pullf.xvg "
33 .BI "\-mtx" " nm.mtx "
34 .BI "\-dn" " dipole.ndx "
35 .BI "\-multidir" " rundir "
37 .BI "\-[no]version" ""
39 .BI "\-deffnm" " string "
45 .BI "\-ddorder" " enum "
46 .BI "\-[no]ddcheck" ""
53 .BI "\-[no]compact" ""
55 .BI "\-pforce" " real "
62 .BI "\-replex" " int "
63 .BI "\-reseed" " int "
66 \&The \fB mdrun\fR program is the main computational chemistry engine
67 \&within GROMACS. Obviously, it performs Molecular Dynamics simulations,
68 \&but it can also perform Stochastic Dynamics, Energy Minimization,
69 \&test particle insertion or (re)calculation of energies.
70 \&Normal mode analysis is another option. In this case \fB mdrun\fR
71 \&builds a Hessian matrix from single conformation.
72 \&For usual Normal Modes\-like calculations, make sure that
73 \&the structure provided is properly energy\-minimized.
74 \&The generated matrix can be diagonalized by \fB g_nmeig\fR.
77 \&The \fB mdrun\fR program reads the run input file (\fB \-s\fR)
78 \&and distributes the topology over nodes if needed.
79 \&\fB mdrun\fR produces at least four output files.
80 \&A single log file (\fB \-g\fR) is written, unless the option
81 \&\fB \-seppot\fR is used, in which case each node writes a log file.
82 \&The trajectory file (\fB \-o\fR), contains coordinates, velocities and
84 \&The structure file (\fB \-c\fR) contains the coordinates and
85 \&velocities of the last step.
86 \&The energy file (\fB \-e\fR) contains energies, the temperature,
87 \&pressure, etc, a lot of these things are also printed in the log file.
88 \&Optionally coordinates can be written to a compressed trajectory file
92 \&The option \fB \-dhdl\fR is only used when free energy calculation is
96 \&When \fB mdrun\fR is started using MPI with more than 1 node, parallelization
97 \&is used. By default domain decomposition is used, unless the \fB \-pd\fR
98 \&option is set, which selects particle decomposition.
101 \&With domain decomposition, the spatial decomposition can be set
102 \&with option \fB \-dd\fR. By default \fB mdrun\fR selects a good decomposition.
103 \&The user only needs to change this when the system is very inhomogeneous.
104 \&Dynamic load balancing is set with the option \fB \-dlb\fR,
105 \&which can give a significant performance improvement,
106 \&especially for inhomogeneous systems. The only disadvantage of
107 \&dynamic load balancing is that runs are no longer binary reproducible,
108 \&but in most cases this is not important.
109 \&By default the dynamic load balancing is automatically turned on
110 \&when the measured performance loss due to load imbalance is 5% or more.
111 \&At low parallelization these are the only important options
112 \&for domain decomposition.
113 \&At high parallelization the options in the next two sections
114 \&could be important for increasing the performace.
118 \&When PME is used with domain decomposition, separate nodes can
119 \&be assigned to do only the PME mesh calculation;
120 \&this is computationally more efficient starting at about 12 nodes.
121 \&The number of PME nodes is set with option \fB \-npme\fR,
122 \&this can not be more than half of the nodes.
123 \&By default \fB mdrun\fR makes a guess for the number of PME
124 \&nodes when the number of nodes is larger than 11 or performance wise
125 \¬ compatible with the PME grid x dimension.
126 \&But the user should optimize npme. Performance statistics on this issue
127 \&are written at the end of the log file.
128 \&For good load balancing at high parallelization, the PME grid x and y
129 \&dimensions should be divisible by the number of PME nodes
130 \&(the simulation will run correctly also when this is not the case).
134 \&This section lists all options that affect the domain decomposition.
138 \&Option \fB \-rdd\fR can be used to set the required maximum distance
139 \&for inter charge\-group bonded interactions.
140 \&Communication for two\-body bonded interactions below the non\-bonded
141 \&cut\-off distance always comes for free with the non\-bonded communication.
142 \&Atoms beyond the non\-bonded cut\-off are only communicated when they have
143 \&missing bonded interactions; this means that the extra cost is minor
144 \&and nearly indepedent of the value of \fB \-rdd\fR.
145 \&With dynamic load balancing option \fB \-rdd\fR also sets
146 \&the lower limit for the domain decomposition cell sizes.
147 \&By default \fB \-rdd\fR is determined by \fB mdrun\fR based on
148 \&the initial coordinates. The chosen value will be a balance
149 \&between interaction range and communication cost.
153 \&When inter charge\-group bonded interactions are beyond
154 \&the bonded cut\-off distance, \fB mdrun\fR terminates with an error message.
155 \&For pair interactions and tabulated bonds
156 \&that do not generate exclusions, this check can be turned off
157 \&with the option \fB \-noddcheck\fR.
161 \&When constraints are present, option \fB \-rcon\fR influences
162 \&the cell size limit as well.
163 \&Atoms connected by NC constraints, where NC is the LINCS order plus 1,
164 \&should not be beyond the smallest cell size. A error message is
165 \&generated when this happens and the user should change the decomposition
166 \&or decrease the LINCS order and increase the number of LINCS iterations.
167 \&By default \fB mdrun\fR estimates the minimum cell size required for P\-LINCS
168 \&in a conservative fashion. For high parallelization it can be useful
169 \&to set the distance required for P\-LINCS with the option \fB \-rcon\fR.
173 \&The \fB \-dds\fR option sets the minimum allowed x, y and/or z scaling
174 \&of the cells with dynamic load balancing. \fB mdrun\fR will ensure that
175 \&the cells can scale down by at least this factor. This option is used
176 \&for the automated spatial decomposition (when not using \fB \-dd\fR)
177 \&as well as for determining the number of grid pulses, which in turn
178 \&sets the minimum allowed cell size. Under certain circumstances
179 \&the value of \fB \-dds\fR might need to be adjusted to account for
180 \&high or low spatial inhomogeneity of the system.
184 \&The option \fB \-gcom\fR can be used to only do global communication
186 \&This can improve performance for highly parallel simulations
187 \&where this global communication step becomes the bottleneck.
188 \&For a global thermostat and/or barostat the temperature
189 \&and/or pressure will also only be updated every \fB \-gcom\fR steps.
190 \&By default it is set to the minimum of nstcalcenergy and nstlist.
193 \&With \fB \-rerun\fR an input trajectory can be given for which
194 \&forces and energies will be (re)calculated. Neighbor searching will be
195 \&performed for every frame, unless \fB nstlist\fR is zero
196 \&(see the \fB .mdp\fR file).
199 \&ED (essential dynamics) sampling is switched on by using the \fB \-ei\fR
200 \&flag followed by an \fB .edi\fR file.
201 \&The \fB .edi\fR file can be produced using options in the essdyn
202 \&menu of the WHAT IF program. \fB mdrun\fR produces a \fB .edo\fR file that
203 \&contains projections of positions, velocities and forces onto selected
207 \&When user\-defined potential functions have been selected in the
208 \&\fB .mdp\fR file the \fB \-table\fR option is used to pass \fB mdrun\fR
209 \&a formatted table with potential functions. The file is read from
210 \&either the current directory or from the \fB GMXLIB\fR directory.
211 \&A number of pre\-formatted tables are presented in the \fB GMXLIB\fR dir,
212 \&for 6\-8, 6\-9, 6\-10, 6\-11, 6\-12 Lennard\-Jones potentials with
214 \&When pair interactions are present, a separate table for pair interaction
215 \&functions is read using the \fB \-tablep\fR option.
218 \&When tabulated bonded functions are present in the topology,
219 \&interaction functions are read using the \fB \-tableb\fR option.
220 \&For each different tabulated interaction type the table file name is
221 \&modified in a different way: before the file extension an underscore is
222 \&appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals
223 \&and finally the table number of the interaction type.
226 \&The options \fB \-px\fR and \fB \-pf\fR are used for writing pull COM
227 \&coordinates and forces when pulling is selected
228 \&in the \fB .mdp\fR file.
231 \&With \fB \-multi\fR or \fB \-multidir\fR, multiple systems can be
232 \&simulated in parallel.
233 \&As many input files/directories are required as the number of systems.
234 \&The \fB \-multidir\fR option takes a list of directories (one for each
235 \&system) and runs in each of them, using the input/output file names,
236 \&such as specified by e.g. the \fB \-s\fR option, relative to these
238 \&With \fB \-multi\fR, the system number is appended to the run input
239 \&and each output filename, for instance \fB topol.tpr\fR becomes
240 \&\fB topol0.tpr\fR, \fB topol1.tpr\fR etc.
241 \&The number of nodes per system is the total number of nodes
242 \÷d by the number of systems.
243 \&One use of this option is for NMR refinement: when distance
244 \&or orientation restraints are present these can be ensemble averaged
245 \&over all the systems.
248 \&With \fB \-replex\fR replica exchange is attempted every given number
249 \&of steps. The number of replicas is set with the \fB \-multi\fR or
250 \&\fB \-multidir\fR option, described above.
251 \&All run input files should use a different coupling temperature,
252 \&the order of the files is not important. The random seed is set with
253 \&\fB \-reseed\fR. The velocities are scaled and neighbor searching
254 \&is performed after every exchange.
257 \&Finally some experimental algorithms can be tested when the
258 \&appropriate options have been given. Currently under
259 \&investigation are: polarizability and X\-ray bombardments.
263 \&The option \fB \-pforce\fR is useful when you suspect a simulation
264 \&crashes due to too large forces. With this option coordinates and
265 \&forces of atoms with a force larger than a certain value will
266 \&be printed to stderr.
270 \&Checkpoints containing the complete state of the system are written
271 \&at regular intervals (option \fB \-cpt\fR) to the file \fB \-cpo\fR,
272 \&unless option \fB \-cpt\fR is set to \-1.
273 \&The previous checkpoint is backed up to \fB state_prev.cpt\fR to
274 \&make sure that a recent state of the system is always available,
275 \&even when the simulation is terminated while writing a checkpoint.
276 \&With \fB \-cpnum\fR all checkpoint files are kept and appended
277 \&with the step number.
278 \&A simulation can be continued by reading the full state from file
279 \&with option \fB \-cpi\fR. This option is intelligent in the way that
280 \&if no checkpoint file is found, Gromacs just assumes a normal run and
281 \&starts from the first step of the \fB .tpr\fR file. By default the output
282 \&will be appending to the existing output files. The checkpoint file
283 \&contains checksums of all output files, such that you will never
284 \&loose data when some output files are modified, corrupt or removed.
285 \&There are three scenarios with \fB \-cpi\fR:
288 \&\fB *\fR no files with matching names are present: new output files are written
291 \&\fB *\fR all files are present with names and checksums matching those stored
292 \&in the checkpoint file: files are appended
295 \&\fB *\fR otherwise no files are modified and a fatal error is generated
298 \&With \fB \-noappend\fR new output files are opened and the simulation
299 \&part number is added to all output file names.
300 \&Note that in all cases the checkpoint file itself is not renamed
301 \&and will be overwritten, unless its name does not match
302 \&the \fB \-cpo\fR option.
306 \&With checkpointing the output is appended to previously written
307 \&output files, unless \fB \-noappend\fR is used or none of the previous
308 \&output files are present (except for the checkpoint file).
309 \&The integrity of the files to be appended is verified using checksums
310 \&which are stored in the checkpoint file. This ensures that output can
311 \¬ be mixed up or corrupted due to file appending. When only some
312 \&of the previous output files are present, a fatal error is generated
313 \&and no old output files are modified and no new output files are opened.
314 \&The result with appending will be the same as from a single run.
315 \&The contents will be binary identical, unless you use a different number
316 \&of nodes or dynamic load balancing or the FFT library uses optimizations
321 \&With option \fB \-maxh\fR a simulation is terminated and a checkpoint
322 \&file is written at the first neighbor search step where the run time
323 \&exceeds \fB \-maxh\fR*0.99 hours.
327 \&When \fB mdrun\fR receives a TERM signal, it will set nsteps to the current
328 \&step plus one. When \fB mdrun\fR receives an INT signal (e.g. when ctrl+C is
329 \&pressed), it will stop after the next neighbor search step
330 \&(with nstlist=0 at the next step).
331 \&In both cases all the usual output will be written to file.
332 \&When running with MPI, a signal to one of the \fB mdrun\fR processes
333 \&is sufficient, this signal should not be sent to mpirun or
334 \&the \fB mdrun\fR process that is the parent of the others.
338 \&When \fB mdrun\fR is started with MPI, it does not run niced by default.
340 .BI "\-s" " topol.tpr"
342 Run input file: tpr tpb tpa
344 .BI "\-o" " traj.trr"
346 Full precision trajectory: trr trj cpt
348 .BI "\-x" " traj.xtc"
350 Compressed trajectory (portable xdr format)
352 .BI "\-cpi" " state.cpt"
356 .BI "\-cpo" " state.cpt"
360 .BI "\-c" " confout.gro"
362 Structure file: gro g96 pdb etc.
364 .BI "\-e" " ener.edr"
372 .BI "\-dhdl" " dhdl.xvg"
376 .BI "\-field" " field.xvg"
380 .BI "\-table" " table.xvg"
384 .BI "\-tablep" " tablep.xvg"
388 .BI "\-tableb" " table.xvg"
392 .BI "\-rerun" " rerun.xtc"
394 Trajectory: xtc trr trj gro g96 pdb cpt
396 .BI "\-tpi" " tpi.xvg"
400 .BI "\-tpid" " tpidist.xvg"
404 .BI "\-ei" " sam.edi"
408 .BI "\-eo" " sam.edo"
412 .BI "\-j" " wham.gct"
414 General coupling stuff
416 .BI "\-jo" " bam.gct"
418 General coupling stuff
420 .BI "\-ffout" " gct.xvg"
424 .BI "\-devout" " deviatie.xvg"
428 .BI "\-runav" " runaver.xvg"
432 .BI "\-px" " pullx.xvg"
436 .BI "\-pf" " pullf.xvg"
440 .BI "\-mtx" " nm.mtx"
444 .BI "\-dn" " dipole.ndx"
448 .BI "\-multidir" " rundir"
449 .B Input, Opt., Mult.
454 Print help info and quit
456 .BI "\-[no]version" "no "
457 Print version info and quit
459 .BI "\-nice" " int" " 0"
462 .BI "\-deffnm" " string" " "
463 Set the default filename for all file options
465 .BI "\-xvg" " enum" " xmgrace"
466 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
469 Use particle decompostion
471 .BI "\-dd" " vector" " 0 0 0"
472 Domain decomposition grid, 0 is optimize
474 .BI "\-nt" " int" " 0"
475 Number of threads to start (0 is guess)
477 .BI "\-npme" " int" " \-1"
478 Number of separate nodes to be used for PME, \-1 is guess
480 .BI "\-ddorder" " enum" " interleave"
481 DD node order: \fB interleave\fR, \fB pp_pme\fR or \fB cartesian\fR
483 .BI "\-[no]ddcheck" "yes "
484 Check for all bonded interactions with DD
486 .BI "\-rdd" " real" " 0 "
487 The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates
489 .BI "\-rcon" " real" " 0 "
490 Maximum distance for P\-LINCS (nm), 0 is estimate
492 .BI "\-dlb" " enum" " auto"
493 Dynamic load balancing (with DD): \fB auto\fR, \fB no\fR or \fB yes\fR
495 .BI "\-dds" " real" " 0.8 "
496 Minimum allowed dlb scaling of the DD cell size
498 .BI "\-gcom" " int" " \-1"
499 Global communication frequency
504 .BI "\-[no]compact" "yes "
505 Write a compact log file
507 .BI "\-[no]seppot" "no "
508 Write separate V and dVdl terms for each interaction type and node to the log file(s)
510 .BI "\-pforce" " real" " \-1 "
511 Print all forces larger than this (kJ/mol nm)
513 .BI "\-[no]reprod" "no "
514 Try to avoid optimizations that affect binary reproducibility
516 .BI "\-cpt" " real" " 15 "
517 Checkpoint interval (minutes)
519 .BI "\-[no]cpnum" "no "
520 Keep and number checkpoint files
522 .BI "\-[no]append" "yes "
523 Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names
525 .BI "\-maxh" " real" " \-1 "
526 Terminate after 0.99 times this time (hours)
528 .BI "\-multi" " int" " 0"
529 Do multiple simulations in parallel
531 .BI "\-replex" " int" " 0"
532 Attempt replica exchange periodically with this period (steps)
534 .BI "\-reseed" " int" " \-1"
535 Seed for replica exchange, \-1 is generate a seed
537 .BI "\-[no]ionize" "no "
538 Do a simulation including the effect of an X\-Ray bombardment on your system
543 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.