1GMX-MDRUN(1) GROMACS GMX-MDRUN(1)
2
6 gmx-mdrun - Perform a simulation, do a normal mode analysis or an en‐
7 ergy 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>]] [-px [<.xvg>]]
19 [-pf [<.xvg>]] [-ro [<.xvg>]] [-ra [<.log>]] [-rs [<.log>]]
20 [-rt [<.log>]] [-mtx [<.mtx>]] [-if [<.xvg>]]
21 [-swap [<.xvg>]] [-deffnm <string>] [-xvg <enum>]
22 [-dd <vector>] [-ddorder <enum>] [-npme <int>] [-nt <int>]
23 [-ntmpi <int>] [-ntomp <int>] [-ntomp_pme <int>]
24 [-pin <enum>] [-pinoffset <int>] [-pinstride <int>]
25 [-gpu_id <string>] [-gputasks <string>] [-[no]ddcheck]
26 [-rdd <real>] [-rcon <real>] [-dlb <enum>] [-dds <real>]
27 [-nb <enum>] [-nstlist <int>] [-[no]tunepme] [-pme <enum>]
28 [-pmefft <enum>] [-bonded <enum>] [-update <enum>] [-[no]v]
29 [-pforce <real>] [-[no]reprod] [-cpt <real>] [-[no]cpnum]
30 [-[no]append] [-nsteps <int>] [-maxh <real>]
31 [-replex <int>] [-nex <int>] [-reseed <int>]
32
34 gmx mdrun is the main computational chemistry engine within GROMACS.
35 Obviously, it performs Molecular Dynamics simulations, but it can also
36 perform Stochastic Dynamics, Energy Minimization, test particle inser‐
37 tion or (re)calculation of energies. Normal mode analysis is another
38 option. In this case mdrun builds a Hessian matrix from single confor‐
39 mation. For usual Normal Modes-like calculations, make sure that the
40 structure provided is properly energy-minimized. The generated matrix
41 can be diagonalized by gmx nmeig.
42 The mdrun program reads the run input file (-s) and distributes the
44 topology over ranks if needed. mdrun produces at least four output
45 files. A single log file (-g) is written. The trajectory file (-o),
46 contains coordinates, velocities and optionally forces. The structure
47 file (-c) contains the coordinates and velocities of the last step.
48 The energy file (-e) contains energies, the temperature, pressure, etc,
49 a lot of these things are also printed in the log file. Optionally co‐
50 ordinates can be written to a compressed trajectory file (-x).
51 The option -dhdl is only used when free energy calculation is turned
53 on.
54 Running mdrun efficiently in parallel is a complex topic, many aspects
56 of which are covered in the online User Guide. You should look there
57 for practical advice on using many of the options available in mdrun.
58 ED (essential dynamics) sampling and/or additional flooding potentials
60 are switched on by using the -ei flag followed by an .edi file. The
61 .edi file can be produced with the make_edi tool or by using options in
62 the essdyn menu of the WHAT IF program. mdrun produces a .xvg output
63 file that contains projections of positions, velocities and forces onto
64 selected eigenvectors.
65 When user-defined potential functions have been selected in the .mdp
67 file the -table option is used to pass mdrun a formatted table with po‐
68 tential functions. The file is read from either the current directory
69 or from the GMXLIB directory. A number of pre-formatted tables are
70 presented in the GMXLIB dir, for 6-8, 6-9, 6-10, 6-11, 6-12
71 Lennard-Jones potentials with normal Coulomb. When pair interactions
72 are present, a separate table for pair interaction functions is read
73 using the -tablep option.
74 When tabulated bonded functions are present in the topology, interac‐
76 tion functions are read using the -tableb option. For each different
77 tabulated interaction type used, a table file name must be given. For
78 the topology to work, a file name given here must match a character se‐
79 quence before the file extension. That sequence is: an underscore, then
80 a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals, and finally
81 the matching table number index used in the topology. Note that, these
82 options are deprecated, and in future will be available via grompp.
83 The options -px and -pf are used for writing pull COM coordinates and
85 forces when pulling is selected in the .mdp file.
86 The option -membed does what used to be g_membed, i.e. embed a protein
88 into a membrane. This module requires a number of settings that are
89 provided in a data file that is the argument of this option. For more
90 details in membrane embedding, see the documentation in the user guide.
91 The options -mn and -mp are used to provide the index and topology
92 files used for the embedding.
93 The option -pforce is useful when you suspect a simulation crashes due
95 to too large forces. With this option coordinates and forces of atoms
96 with a force larger than a certain value will be printed to stderr. It
97 will also terminate the run when non-finite forces are present.
98 Checkpoints containing the complete state of the system are written at
100 regular intervals (option -cpt) to the file -cpo, unless option -cpt is
101 set to -1. The previous checkpoint is backed up to state_prev.cpt to
102 make sure that a recent state of the system is always available, even
103 when the simulation is terminated while writing a checkpoint. With
104 -cpnum all checkpoint files are kept and appended with the step number.
105 A simulation can be continued by reading the full state from file with
106 option -cpi. This option is intelligent in the way that if no check‐
107 point file is found, GROMACS just assumes a normal run and starts from
108 the first step of the .tpr file. By default the output will be append‐
109 ing to the existing output files. The checkpoint file contains check‐
110 sums of all output files, such that you will never loose data when some
111 output files are modified, corrupt or removed. There are three scenar‐
112 ios with -cpi:
113 * no files with matching names are present: new output files are writ‐
115 ten
116 * all files are present with names and checksums matching those stored
118 in the checkpoint file: files are appended
119 * otherwise no files are modified and a fatal error is generated
121 With -noappend new output files are opened and the simulation part num‐
123 ber is added to all output file names. Note that in all cases the
124 checkpoint file itself is not renamed and will be overwritten, unless
125 its name does not match the -cpo option.
126 With checkpointing the output is appended to previously written output
128 files, unless -noappend is used or none of the previous output files
129 are present (except for the checkpoint file). The integrity of the
130 files to be appended is verified using checksums which are stored in
131 the checkpoint file. This ensures that output can not be mixed up or
132 corrupted due to file appending. When only some of the previous output
133 files are present, a fatal error is generated and no old output files
134 are modified and no new output files are opened. The result with ap‐
135 pending will be the same as from a single run. The contents will be
136 binary identical, unless you use a different number of ranks or dynamic
137 load balancing or the FFT library uses optimizations through timing.
138 With option -maxh a simulation is terminated and a checkpoint file is
140 written at the first neighbor search step where the run time exceeds
141 -maxh*0.99 hours. This option is particularly useful in combination
142 with setting nsteps to -1 either in the mdp or using the similarly
143 named command line option (although the latter is deprecated). This
144 results in an infinite run, terminated only when the time limit set by
145 -maxh is reached (if any) or upon receiving a signal.
146 Interactive molecular dynamics (IMD) can be activated by using at least
148 one of the three IMD switches: The -imdterm switch allows one to termi‐
149 nate the simulation from the molecular viewer (e.g. VMD). With -imd‐
150 wait, mdrun pauses whenever no IMD client is connected. Pulling from
151 the IMD remote can be turned on by -imdpull. The port mdrun listens to
152 can be altered by -imdport.The file pointed to by -if contains atom in‐
153 dices and forces if IMD pulling is used.
154
156 Options to specify input files:
157 -s [<.tpr>] (topol.tpr)
159 Portable xdr run input file
160 -cpi [<.cpt>] (state.cpt) (Optional)
162 Checkpoint file
163 -table [<.xvg>] (table.xvg) (Optional)
165 xvgr/xmgr file
166 -tablep [<.xvg>] (tablep.xvg) (Optional)
168 xvgr/xmgr file
169 -tableb [<.xvg> [...]] (table.xvg) (Optional)
171 xvgr/xmgr file
172 -rerun [<.xtc/.trr/...>] (rerun.xtc) (Optional)
174 Trajectory: xtc trr cpt gro g96 pdb tng
175 -ei [<.edi>] (sam.edi) (Optional)
177 ED sampling input
178 -multidir [<dir> [...]] (rundir) (Optional)
180 Run directory
181 -awh [<.xvg>] (awhinit.xvg) (Optional)
183 xvgr/xmgr file
184 -membed [<.dat>] (membed.dat) (Optional)
186 Generic data file
187 -mp [<.top>] (membed.top) (Optional)
189 Topology file
190 -mn [<.ndx>] (membed.ndx) (Optional)
192 Index file
193 Options to specify output files:
195 -o [<.trr/.cpt/...>] (traj.trr)
197 Full precision trajectory: trr cpt tng
198 -x [<.xtc/.tng>] (traj_comp.xtc) (Optional)
200 Compressed trajectory (tng format or portable xdr format)
201 -cpo [<.cpt>] (state.cpt) (Optional)
203 Checkpoint file
204 -c [<.gro/.g96/...>] (confout.gro)
206 Structure file: gro g96 pdb brk ent esp
207 -e [<.edr>] (ener.edr)
209 Energy file
210 -g [<.log>] (md.log)
212 Log file
213 -dhdl [<.xvg>] (dhdl.xvg) (Optional)
215 xvgr/xmgr file
216 -field [<.xvg>] (field.xvg) (Optional)
218 xvgr/xmgr file
219 -tpi [<.xvg>] (tpi.xvg) (Optional)
221 xvgr/xmgr file
222 -tpid [<.xvg>] (tpidist.xvg) (Optional)
224 xvgr/xmgr file
225 -eo [<.xvg>] (edsam.xvg) (Optional)
227 xvgr/xmgr file
228 -px [<.xvg>] (pullx.xvg) (Optional)
230 xvgr/xmgr file
231 -pf [<.xvg>] (pullf.xvg) (Optional)
233 xvgr/xmgr file
234 -ro [<.xvg>] (rotation.xvg) (Optional)
236 xvgr/xmgr file
237 -ra [<.log>] (rotangles.log) (Optional)
239 Log file
240 -rs [<.log>] (rotslabs.log) (Optional)
242 Log file
243 -rt [<.log>] (rottorque.log) (Optional)
245 Log file
246 -mtx [<.mtx>] (nm.mtx) (Optional)
248 Hessian matrix
249 -if [<.xvg>] (imdforces.xvg) (Optional)
251 xvgr/xmgr file
252 -swap [<.xvg>] (swapions.xvg) (Optional)
254 xvgr/xmgr file
255 Other options:
257 -deffnm <string>
259 Set the default filename for all file options
260 -xvg <enum> (xmgrace)
262 xvg plot formatting: xmgrace, xmgr, none
263 -dd <vector> (0 0 0)
265 Domain decomposition grid, 0 is optimize
266 -ddorder <enum> (interleave)
268 DD rank order: interleave, pp_pme, cartesian
269 -npme <int> (-1)
271 Number of separate ranks to be used for PME, -1 is guess
272 -nt <int> (0)
274 Total number of threads to start (0 is guess)
275 -ntmpi <int> (0)
277 Number of thread-MPI ranks to start (0 is guess)
278 -ntomp <int> (0)
280 Number of OpenMP threads per MPI rank to start (0 is guess)
281 -ntomp_pme <int> (0)
283 Number of OpenMP threads per MPI rank to start (0 is -ntomp)
284 -pin <enum> (auto)
286 Whether mdrun should try to set thread affinities: auto, on, off
287 -pinoffset <int> (0)
289 The lowest logical core number to which mdrun should pin the
290 first thread
291 -pinstride <int> (0)
293 Pinning distance in logical cores for threads, use 0 to minimize
294 the number of threads per physical core
295 -gpu_id <string>
297 List of unique GPU device IDs available to use
298 -gputasks <string>
300 List of GPU device IDs, mapping each PP task on each node to a
301 device
302 -[no]ddcheck (yes)
304 Check for all bonded interactions with DD
305 -rdd <real> (0)
307 The maximum distance for bonded interactions with DD (nm), 0 is
308 determine from initial coordinates
309 -rcon <real> (0)
311 Maximum distance for P-LINCS (nm), 0 is estimate
312 -dlb <enum> (auto)
314 Dynamic load balancing (with DD): auto, no, yes
315 -dds <real> (0.8)
317 Fraction in (0,1) by whose reciprocal the initial DD cell size
318 will be increased in order to provide a margin in which dynamic
319 load balancing can act while preserving the minimum cell size.
320 -nb <enum> (auto)
322 Calculate non-bonded interactions on: auto, cpu, gpu
323 -nstlist <int> (0)
325 Set nstlist when using a Verlet buffer tolerance (0 is guess)
326 -[no]tunepme (yes)
328 Optimize PME load between PP/PME ranks or GPU/CPU
329 -pme <enum> (auto)
331 Perform PME calculations on: auto, cpu, gpu
332 -pmefft <enum> (auto)
334 Perform PME FFT calculations on: auto, cpu, gpu
335 -bonded <enum> (auto)
337 Perform bonded calculations on: auto, cpu, gpu
338 -update <enum> (auto)
340 Perform update and constraints on: auto, cpu, gpu
341 -[no]v (no)
343 Be loud and noisy
344 -pforce <real> (-1)
346 Print all forces larger than this (kJ/mol nm)
347 -[no]reprod (no)
349 Try to avoid optimizations that affect binary reproducibility
350 -cpt <real> (15)
352 Checkpoint interval (minutes)
353 -[no]cpnum (no)
355 Keep and number checkpoint files
356 -[no]append (yes)
358 Append to previous output files when continuing from checkpoint
359 instead of adding the simulation part number to all file names
360 -nsteps <int> (-2)
362 Run this number of steps (-1 means infinite, -2 means use mdp
363 option, smaller is invalid)
364 -maxh <real> (-1)
366 Terminate after 0.99 times this time (hours)
367 -replex <int> (0)
369 Attempt replica exchange periodically with this period (steps)
370 -nex <int> (0)
372 Number of random exchanges to carry out each exchange interval
373 (N^3 is one suggestion). -nex zero or not specified gives
374 neighbor replica exchange.
375 -reseed <int> (-1)
377 Seed for replica exchange, -1 is generate a seed
378
380 gmx(1)
381 More information about GROMACS is available at <‐
383 http://www.gromacs.org/>.
384
386 2022, GROMACS development team
3872022.3 Sep 02, 2022 GMX-MDRUN(1)