1GMX-MDRUN(1) GROMACS GMX-MDRUN(1)
2
6 gmx-mdrun - Perform a simulation, do a normal mode analysis or an
7 energy minimization
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10 gmx mdrun [-s [<.tpr>]] [-cpi [<.cpt>]] [-table [<.xvg>]]
11 [-tablep [<.xvg>]] [-tableb [<.xvg> [...]]]
12 [-rerun [<.xtc/.trr/...>]] [-ei [<.edi>]]
13 [-multidir [<dir> [...]]] [-awh [<.xvg>]]
14 [-membed [<.dat>]] [-mp [<.top>]] [-mn [<.ndx>]]
15 [-o [<.trr/.cpt/...>]] [-x [<.xtc/.tng>]] [-cpo [<.cpt>]]
16 [-c [<.gro/.g96/...>]] [-e [<.edr>]] [-g [<.log>]]
17 [-dhdl [<.xvg>]] [-field [<.xvg>]] [-tpi [<.xvg>]]
18 [-tpid [<.xvg>]] [-eo [<.xvg>]] [-devout [<.xvg>]]
19 [-runav [<.xvg>]] [-px [<.xvg>]] [-pf [<.xvg>]]
20 [-ro [<.xvg>]] [-ra [<.log>]] [-rs [<.log>]] [-rt [<.log>]]
21 [-mtx [<.mtx>]] [-if [<.xvg>]] [-swap [<.xvg>]]
22 [-deffnm <string>] [-xvg <enum>] [-dd <vector>]
23 [-ddorder <enum>] [-npme <int>] [-nt <int>] [-ntmpi <int>]
24 [-ntomp <int>] [-ntomp_pme <int>] [-pin <enum>]
25 [-pinoffset <int>] [-pinstride <int>] [-gpu_id <string>]
26 [-gputasks <string>] [-[no]ddcheck] [-rdd <real>]
27 [-rcon <real>] [-dlb <enum>] [-dds <real>] [-gcom <int>]
28 [-nb <enum>] [-nstlist <int>] [-[no]tunepme] [-pme <enum>]
29 [-pmefft <enum>] [-bonded <enum>] [-[no]v] [-pforce <real>]
30 [-[no]reprod] [-cpt <real>] [-[no]cpnum] [-[no]append]
31 [-nsteps <int>] [-maxh <real>] [-replex <int>] [-nex <int>]
32 [-reseed <int>]
33
35 gmx mdrun is the main computational chemistry engine within GROMACS.
36 Obviously, it performs Molecular Dynamics simulations, but it can also
37 perform Stochastic Dynamics, Energy Minimization, test particle inser‐
38 tion or (re)calculation of energies. Normal mode analysis is another
39 option. In this case mdrun builds a Hessian matrix from single confor‐
40 mation. For usual Normal Modes-like calculations, make sure that the
41 structure provided is properly energy-minimized. The generated matrix
42 can be diagonalized by gmx nmeig.
43 The mdrun program reads the run input file (-s) and distributes the
45 topology over ranks if needed. mdrun produces at least four output
46 files. A single log file (-g) is written. The trajectory file (-o),
47 contains coordinates, velocities and optionally forces. The structure
48 file (-c) contains the coordinates and velocities of the last step.
49 The energy file (-e) contains energies, the temperature, pressure, etc,
50 a lot of these things are also printed in the log file. Optionally
51 coordinates can be written to a compressed trajectory file (-x).
52 The option -dhdl is only used when free energy calculation is turned
54 on.
55 Running mdrun efficiently in parallel is a complex topic topic, many
57 aspects of which are covered in the online User Guide. You should look
58 there for practical advice on using many of the options available in
59 mdrun.
60 ED (essential dynamics) sampling and/or additional flooding potentials
62 are switched on by using the -ei flag followed by an .edi file. The
63 .edi file can be produced with the make_edi tool or by using options in
64 the essdyn menu of the WHAT IF program. mdrun produces a .xvg output
65 file that contains projections of positions, velocities and forces onto
66 selected eigenvectors.
67 When user-defined potential functions have been selected in the .mdp
69 file the -table option is used to pass mdrun a formatted table with
70 potential functions. The file is read from either the current directory
71 or from the GMXLIB directory. A number of pre-formatted tables are
72 presented in the GMXLIB dir, for 6-8, 6-9, 6-10, 6-11, 6-12
73 Lennard-Jones potentials with normal Coulomb. When pair interactions
74 are present, a separate table for pair interaction functions is read
75 using the -tablep option.
76 When tabulated bonded functions are present in the topology, interac‐
78 tion functions are read using the -tableb option. For each different
79 tabulated interaction type used, a table file name must be given. For
80 the topology to work, a file name given here must match a character
81 sequence before the file extension. That sequence is: an underscore,
82 then a ‘b’ for bonds, an ‘a’ for angles or a ‘d’ for dihedrals, and
83 finally the matching table number index used in the topology. Note
84 that, these options are deprecated, and in future will be available via
85 grompp.
86 The options -px and -pf are used for writing pull COM coordinates and
88 forces when pulling is selected in the .mdp file.
89 Finally some experimental algorithms can be tested when the appropriate
91 options have been given. Currently under investigation are: polariz‐
92 ability.
93 The option -membed does what used to be g_membed, i.e. embed a protein
95 into a membrane. This module requires a number of settings that are
96 provided in a data file that is the argument of this option. For more
97 details in membrane embedding, see the documentation in the user guide.
98 The options -mn and -mp are used to provide the index and topology
99 files used for the embedding.
100 The option -pforce is useful when you suspect a simulation crashes due
102 to too large forces. With this option coordinates and forces of atoms
103 with a force larger than a certain value will be printed to stderr. It
104 will also terminate the run when non-finite forces are present.
105 Checkpoints containing the complete state of the system are written at
107 regular intervals (option -cpt) to the file -cpo, unless option -cpt is
108 set to -1. The previous checkpoint is backed up to state_prev.cpt to
109 make sure that a recent state of the system is always available, even
110 when the simulation is terminated while writing a checkpoint. With
111 -cpnum all checkpoint files are kept and appended with the step number.
112 A simulation can be continued by reading the full state from file with
113 option -cpi. This option is intelligent in the way that if no check‐
114 point file is found, GROMACS just assumes a normal run and starts from
115 the first step of the .tpr file. By default the output will be append‐
116 ing to the existing output files. The checkpoint file contains check‐
117 sums of all output files, such that you will never loose data when some
118 output files are modified, corrupt or removed. There are three scenar‐
119 ios with -cpi:
120 * no files with matching names are present: new output files are writ‐
122 ten
123 * all files are present with names and checksums matching those stored
125 in the checkpoint file: files are appended
126 * otherwise no files are modified and a fatal error is generated
128 With -noappend new output files are opened and the simulation part num‐
130 ber is added to all output file names. Note that in all cases the
131 checkpoint file itself is not renamed and will be overwritten, unless
132 its name does not match the -cpo option.
133 With checkpointing the output is appended to previously written output
135 files, unless -noappend is used or none of the previous output files
136 are present (except for the checkpoint file). The integrity of the
137 files to be appended is verified using checksums which are stored in
138 the checkpoint file. This ensures that output can not be mixed up or
139 corrupted due to file appending. When only some of the previous output
140 files are present, a fatal error is generated and no old output files
141 are modified and no new output files are opened. The result with
142 appending will be the same as from a single run. The contents will be
143 binary identical, unless you use a different number of ranks or dynamic
144 load balancing or the FFT library uses optimizations through timing.
145 With option -maxh a simulation is terminated and a checkpoint file is
147 written at the first neighbor search step where the run time exceeds
148 -maxh*0.99 hours. This option is particularly useful in combination
149 with setting nsteps to -1 either in the mdp or using the similarly
150 named command line option (although the latter is deprecated). This
151 results in an infinite run, terminated only when the time limit set by
152 -maxh is reached (if any) or upon receiving a signal.
153 When mdrun receives a TERM or INT signal (e.g. when ctrl+C is pressed),
155 it will stop at the next neighbor search step or at the second global
156 communication step, whichever happens later. When mdrun receives a
157 second TERM or INT signal and reproducibility is not requested, it will
158 stop at the first global communication step. In both cases all the
159 usual output will be written to file and a checkpoint file is written
160 at the last step. When mdrun receives an ABRT signal or the third TERM
161 or INT signal, it will abort directly without writing a new checkpoint
162 file. When running with MPI, a signal to one of the mdrun ranks is
163 sufficient, this signal should not be sent to mpirun or the mdrun
164 process that is the parent of the others.
165 Interactive molecular dynamics (IMD) can be activated by using at least
167 one of the three IMD switches: The -imdterm switch allows one to termi‐
168 nate the simulation from the molecular viewer (e.g. VMD). With -imd‐
169 wait, mdrun pauses whenever no IMD client is connected. Pulling from
170 the IMD remote can be turned on by -imdpull. The port mdrun listens to
171 can be altered by -imdport.The file pointed to by -if contains atom
172 indices and forces if IMD pulling is used.
173 When mdrun is started with MPI, it does not run niced by default.
175
177 Options to specify input files:
178 -s [<.tpr>] (topol.tpr)
180 Portable xdr run input file
181 -cpi [<.cpt>] (state.cpt) (Optional)
183 Checkpoint file
184 -table [<.xvg>] (table.xvg) (Optional)
186 xvgr/xmgr file
187 -tablep [<.xvg>] (tablep.xvg) (Optional)
189 xvgr/xmgr file
190 -tableb [<.xvg> […]] (table.xvg) (Optional)
192 xvgr/xmgr file
193 -rerun [<.xtc/.trr/…>] (rerun.xtc) (Optional)
195 Trajectory: xtc trr cpt gro g96 pdb tng
196 -ei [<.edi>] (sam.edi) (Optional)
198 ED sampling input
199 -multidir [<dir> […]] (rundir) (Optional)
201 Run directory
202 -awh [<.xvg>] (awhinit.xvg) (Optional)
204 xvgr/xmgr file
205 -membed [<.dat>] (membed.dat) (Optional)
207 Generic data file
208 -mp [<.top>] (membed.top) (Optional)
210 Topology file
211 -mn [<.ndx>] (membed.ndx) (Optional)
213 Index file
214 Options to specify output files:
216 -o [<.trr/.cpt/…>] (traj.trr)
218 Full precision trajectory: trr cpt tng
219 -x [<.xtc/.tng>] (traj_comp.xtc) (Optional)
221 Compressed trajectory (tng format or portable xdr format)
222 -cpo [<.cpt>] (state.cpt) (Optional)
224 Checkpoint file
225 -c [<.gro/.g96/…>] (confout.gro)
227 Structure file: gro g96 pdb brk ent esp
228 -e [<.edr>] (ener.edr)
230 Energy file
231 -g [<.log>] (md.log)
233 Log file
234 -dhdl [<.xvg>] (dhdl.xvg) (Optional)
236 xvgr/xmgr file
237 -field [<.xvg>] (field.xvg) (Optional)
239 xvgr/xmgr file
240 -tpi [<.xvg>] (tpi.xvg) (Optional)
242 xvgr/xmgr file
243 -tpid [<.xvg>] (tpidist.xvg) (Optional)
245 xvgr/xmgr file
246 -eo [<.xvg>] (edsam.xvg) (Optional)
248 xvgr/xmgr file
249 -devout [<.xvg>] (deviatie.xvg) (Optional)
251 xvgr/xmgr file
252 -runav [<.xvg>] (runaver.xvg) (Optional)
254 xvgr/xmgr file
255 -px [<.xvg>] (pullx.xvg) (Optional)
257 xvgr/xmgr file
258 -pf [<.xvg>] (pullf.xvg) (Optional)
260 xvgr/xmgr file
261 -ro [<.xvg>] (rotation.xvg) (Optional)
263 xvgr/xmgr file
264 -ra [<.log>] (rotangles.log) (Optional)
266 Log file
267 -rs [<.log>] (rotslabs.log) (Optional)
269 Log file
270 -rt [<.log>] (rottorque.log) (Optional)
272 Log file
273 -mtx [<.mtx>] (nm.mtx) (Optional)
275 Hessian matrix
276 -if [<.xvg>] (imdforces.xvg) (Optional)
278 xvgr/xmgr file
279 -swap [<.xvg>] (swapions.xvg) (Optional)
281 xvgr/xmgr file
282 Other options:
284 -deffnm <string>
286 Set the default filename for all file options
287 -xvg <enum> (xmgrace)
289 xvg plot formatting: xmgrace, xmgr, none
290 -dd <vector> (0 0 0)
292 Domain decomposition grid, 0 is optimize
293 -ddorder <enum> (interleave)
295 DD rank order: interleave, pp_pme, cartesian
296 -npme <int> (-1)
298 Number of separate ranks to be used for PME, -1 is guess
299 -nt <int> (0)
301 Total number of threads to start (0 is guess)
302 -ntmpi <int> (0)
304 Number of thread-MPI ranks to start (0 is guess)
305 -ntomp <int> (0)
307 Number of OpenMP threads per MPI rank to start (0 is guess)
308 -ntomp_pme <int> (0)
310 Number of OpenMP threads per MPI rank to start (0 is -ntomp)
311 -pin <enum> (auto)
313 Whether mdrun should try to set thread affinities: auto, on, off
314 -pinoffset <int> (0)
316 The lowest logical core number to which mdrun should pin the
317 first thread
318 -pinstride <int> (0)
320 Pinning distance in logical cores for threads, use 0 to minimize
321 the number of threads per physical core
322 -gpu_id <string>
324 List of unique GPU device IDs available to use
325 -gputasks <string>
327 List of GPU device IDs, mapping each PP task on each node to a
328 device
329 -[no]ddcheck (yes)
331 Check for all bonded interactions with DD
332 -rdd <real> (0)
334 The maximum distance for bonded interactions with DD (nm), 0 is
335 determine from initial coordinates
336 -rcon <real> (0)
338 Maximum distance for P-LINCS (nm), 0 is estimate
339 -dlb <enum> (auto)
341 Dynamic load balancing (with DD): auto, no, yes
342 -dds <real> (0.8)
344 Fraction in (0,1) by whose reciprocal the initial DD cell size
345 will be increased in order to provide a margin in which dynamic
346 load balancing can act while preserving the minimum cell size.
347 -gcom <int> (-1)
349 Global communication frequency
350 -nb <enum> (auto)
352 Calculate non-bonded interactions on: auto, cpu, gpu
353 -nstlist <int> (0)
355 Set nstlist when using a Verlet buffer tolerance (0 is guess)
356 -[no]tunepme (yes)
358 Optimize PME load between PP/PME ranks or GPU/CPU (only with the
359 Verlet cut-off scheme)
360 -pme <enum> (auto)
362 Perform PME calculations on: auto, cpu, gpu
363 -pmefft <enum> (auto)
365 Perform PME FFT calculations on: auto, cpu, gpu
366 -bonded <enum> (auto)
368 Perform bonded calculations on: auto, cpu, gpu
369 -[no]v (no)
371 Be loud and noisy
372 -pforce <real> (-1)
374 Print all forces larger than this (kJ/mol nm)
375 -[no]reprod (no)
377 Try to avoid optimizations that affect binary reproducibility
378 -cpt <real> (15)
380 Checkpoint interval (minutes)
381 -[no]cpnum (no)
383 Keep and number checkpoint files
384 -[no]append (yes)
386 Append to previous output files when continuing from checkpoint
387 instead of adding the simulation part number to all file names
388 -nsteps <int> (-2)
390 Run this number of steps (-1 means infinite, -2 means use mdp
391 option, smaller is invalid)
392 -maxh <real> (-1)
394 Terminate after 0.99 times this time (hours)
395 -replex <int> (0)
397 Attempt replica exchange periodically with this period (steps)
398 -nex <int> (0)
400 Number of random exchanges to carry out each exchange interval
401 (N^3 is one suggestion). -nex zero or not specified gives
402 neighbor replica exchange.
403 -reseed <int> (-1)
405 Seed for replica exchange, -1 is generate a seed
406
408 gmx(1)
409 More information about GROMACS is available at <‐
411 http://www.gromacs.org/>.
412
414 2020, GROMACS development team
4152019.6 Feb 28, 2020 GMX-MDRUN(1)