1GMX-MDRUN(1)                        GROMACS                       GMX-MDRUN(1)
2
3
4

NAME

6       gmx-mdrun  -  Perform a simulation, do a normal mode analysis or an en‐
7       ergy minimization
8

SYNOPSIS

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

DESCRIPTION

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
43       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
52       The option -dhdl is only used when free energy  calculation  is  turned
53       on.
54
55       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
59       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
66       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
75       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
84       The options -px and -pf are used for writing pull COM  coordinates  and
85       forces when pulling is selected in the .mdp file.
86
87       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
94       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
99       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
114       * no files with matching names are present: new output files are  writ‐
115       ten
116
117       *  all files are present with names and checksums matching those stored
118       in the checkpoint file: files are appended
119
120       * otherwise no files are modified and a fatal error is generated
121
122       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
127       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
139       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
147       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

OPTIONS

156       Options to specify input files:
157
158       -s [<.tpr>] (topol.tpr)
159              Portable xdr run input file
160
161       -cpi [<.cpt>] (state.cpt) (Optional)
162              Checkpoint file
163
164       -table [<.xvg>] (table.xvg) (Optional)
165              xvgr/xmgr file
166
167       -tablep [<.xvg>] (tablep.xvg) (Optional)
168              xvgr/xmgr file
169
170       -tableb [<.xvg> [...]] (table.xvg) (Optional)
171              xvgr/xmgr file
172
173       -rerun [<.xtc/.trr/...>] (rerun.xtc) (Optional)
174              Trajectory: xtc trr cpt gro g96 pdb tng
175
176       -ei [<.edi>] (sam.edi) (Optional)
177              ED sampling input
178
179       -multidir [<dir> [...]] (rundir) (Optional)
180              Run directory
181
182       -awh [<.xvg>] (awhinit.xvg) (Optional)
183              xvgr/xmgr file
184
185       -membed [<.dat>] (membed.dat) (Optional)
186              Generic data file
187
188       -mp [<.top>] (membed.top) (Optional)
189              Topology file
190
191       -mn [<.ndx>] (membed.ndx) (Optional)
192              Index file
193
194       Options to specify output files:
195
196       -o [<.trr/.cpt/...>] (traj.trr)
197              Full precision trajectory: trr cpt tng
198
199       -x [<.xtc/.tng>] (traj_comp.xtc) (Optional)
200              Compressed trajectory (tng format or portable xdr format)
201
202       -cpo [<.cpt>] (state.cpt) (Optional)
203              Checkpoint file
204
205       -c [<.gro/.g96/...>] (confout.gro)
206              Structure file: gro g96 pdb brk ent esp
207
208       -e [<.edr>] (ener.edr)
209              Energy file
210
211       -g [<.log>] (md.log)
212              Log file
213
214       -dhdl [<.xvg>] (dhdl.xvg) (Optional)
215              xvgr/xmgr file
216
217       -field [<.xvg>] (field.xvg) (Optional)
218              xvgr/xmgr file
219
220       -tpi [<.xvg>] (tpi.xvg) (Optional)
221              xvgr/xmgr file
222
223       -tpid [<.xvg>] (tpidist.xvg) (Optional)
224              xvgr/xmgr file
225
226       -eo [<.xvg>] (edsam.xvg) (Optional)
227              xvgr/xmgr file
228
229       -px [<.xvg>] (pullx.xvg) (Optional)
230              xvgr/xmgr file
231
232       -pf [<.xvg>] (pullf.xvg) (Optional)
233              xvgr/xmgr file
234
235       -ro [<.xvg>] (rotation.xvg) (Optional)
236              xvgr/xmgr file
237
238       -ra [<.log>] (rotangles.log) (Optional)
239              Log file
240
241       -rs [<.log>] (rotslabs.log) (Optional)
242              Log file
243
244       -rt [<.log>] (rottorque.log) (Optional)
245              Log file
246
247       -mtx [<.mtx>] (nm.mtx) (Optional)
248              Hessian matrix
249
250       -if [<.xvg>] (imdforces.xvg) (Optional)
251              xvgr/xmgr file
252
253       -swap [<.xvg>] (swapions.xvg) (Optional)
254              xvgr/xmgr file
255
256       Other options:
257
258       -deffnm <string>
259              Set the default filename for all file options
260
261       -xvg <enum> (xmgrace)
262              xvg plot formatting: xmgrace, xmgr, none
263
264       -dd <vector> (0 0 0)
265              Domain decomposition grid, 0 is optimize
266
267       -ddorder <enum> (interleave)
268              DD rank order: interleave, pp_pme, cartesian
269
270       -npme <int> (-1)
271              Number of separate ranks to be used for PME, -1 is guess
272
273       -nt <int> (0)
274              Total number of threads to start (0 is guess)
275
276       -ntmpi <int> (0)
277              Number of thread-MPI ranks to start (0 is guess)
278
279       -ntomp <int> (0)
280              Number of OpenMP threads per MPI rank to start (0 is guess)
281
282       -ntomp_pme <int> (0)
283              Number of OpenMP threads per MPI rank to start (0 is -ntomp)
284
285       -pin <enum> (auto)
286              Whether mdrun should try to set thread affinities: auto, on, off
287
288       -pinoffset <int> (0)
289              The  lowest  logical  core  number to which mdrun should pin the
290              first thread
291
292       -pinstride <int> (0)
293              Pinning distance in logical cores for threads, use 0 to minimize
294              the number of threads per physical core
295
296       -gpu_id <string>
297              List of unique GPU device IDs available to use
298
299       -gputasks <string>
300              List  of  GPU device IDs, mapping each PP task on each node to a
301              device
302
303       -[no]ddcheck (yes)
304              Check for all bonded interactions with DD
305
306       -rdd <real> (0)
307              The maximum distance for bonded interactions with DD (nm), 0  is
308              determine from initial coordinates
309
310       -rcon <real> (0)
311              Maximum distance for P-LINCS (nm), 0 is estimate
312
313       -dlb <enum> (auto)
314              Dynamic load balancing (with DD): auto, no, yes
315
316       -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
321       -nb <enum> (auto)
322              Calculate non-bonded interactions on: auto, cpu, gpu
323
324       -nstlist <int> (0)
325              Set nstlist when using a Verlet buffer tolerance (0 is guess)
326
327       -[no]tunepme (yes)
328              Optimize PME load between PP/PME ranks or GPU/CPU
329
330       -pme <enum> (auto)
331              Perform PME calculations on: auto, cpu, gpu
332
333       -pmefft <enum> (auto)
334              Perform PME FFT calculations on: auto, cpu, gpu
335
336       -bonded <enum> (auto)
337              Perform bonded calculations on: auto, cpu, gpu
338
339       -update <enum> (auto)
340              Perform update and constraints on: auto, cpu, gpu
341
342       -[no]v (no)
343              Be loud and noisy
344
345       -pforce <real> (-1)
346              Print all forces larger than this (kJ/mol nm)
347
348       -[no]reprod (no)
349              Try to avoid optimizations that affect binary reproducibility
350
351       -cpt <real> (15)
352              Checkpoint interval (minutes)
353
354       -[no]cpnum (no)
355              Keep and number checkpoint files
356
357       -[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
361       -nsteps <int> (-2)
362              Run this number of steps (-1 means infinite, -2  means  use  mdp
363              option, smaller is invalid)
364
365       -maxh <real> (-1)
366              Terminate after 0.99 times this time (hours)
367
368       -replex <int> (0)
369              Attempt replica exchange periodically with this period (steps)
370
371       -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
376       -reseed <int> (-1)
377              Seed for replica exchange, -1 is generate a seed
378

SEE ALSO

380       gmx(1)
381
382       More     information    about    GROMACS    is    available    at    <‐
383       http://www.gromacs.org/>.
384
386       2022, GROMACS development team
387
388
389
390
3912022.3                           Sep 02, 2022                     GMX-MDRUN(1)
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