1GMX-GROMPP(1)                       GROMACS                      GMX-GROMPP(1)
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NAME

6       gmx-grompp - Make a run input file
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SYNOPSIS

9          gmx grompp [-f [<.mdp>]] [-c [<.gro/.g96/...>]] [-r [<.gro/.g96/...>]]
10                     [-rb [<.gro/.g96/...>]] [-n [<.ndx>]] [-p [<.top>]]
11                     [-t [<.trr/.cpt/...>]] [-e [<.edr>]]
12                     [-ref [<.trr/.cpt/...>]] [-po [<.mdp>]] [-pp [<.top>]]
13                     [-o [<.tpr>]] [-imd [<.gro>]] [-[no]v] [-time <real>]
14                     [-[no]rmvsbds] [-maxwarn <int>] [-[no]zero] [-[no]renum]
15

DESCRIPTION

17       gmx  grompp (the gromacs preprocessor) reads a molecular topology file,
18       checks the validity of the file, expands the topology from a  molecular
19       description to an atomic description. The topology file contains infor‐
20       mation about molecule types and the number of molecules, the preproces‐
21       sor copies each molecule as needed.  There is no limitation on the num‐
22       ber of molecule types.  Bonds and bond-angles  can  be  converted  into
23       constraints,  separately for hydrogens and heavy atoms.  Then a coordi‐
24       nate file is read and velocities can be  generated  from  a  Maxwellian
25       distribution  if  requested.   gmx grompp also reads parameters for gmx
26       mdrun (eg. number of MD steps, time step, cut-off), and others such  as
27       NEMD  parameters,  which  are corrected so that the net acceleration is
28       zero.  Eventually a binary file is produced that can serve as the  sole
29       input file for the MD program.
30
31       gmx  grompp  uses the atom names from the topology file. The atom names
32       in the coordinate file (option -c) are only read to  generate  warnings
33       when  they  do not match the atom names in the topology.  Note that the
34       atom names are irrelevant for the simulation as only the atom types are
35       used for generating interaction parameters.
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37       gmx  grompp  uses  a built-in preprocessor to resolve includes, macros,
38       etc. The preprocessor supports the following keywords:
39
40          #ifdef VARIABLE
41          #ifndef VARIABLE
42          #else
43          #endif
44          #define VARIABLE
45          #undef VARIABLE
46          #include "filename"
47          #include <filename>
48
49       The functioning of these statements in your topology may  be  modulated
50       by using the following two flags in your .mdp file:
51
52          define = -DVARIABLE1 -DVARIABLE2
53          include = -I/home/john/doe
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55       For  further  information  a  C-programming  textbook may help you out.
56       Specifying the -pp flag will get the pre-processed topology file  writ‐
57       ten out so that you can verify its contents.
58
59       When  using position restraints, a file with restraint coordinates must
60       be supplied with -r (can be the same file as supplied for -c). For free
61       energy  calculations, separate reference coordinates for the B topology
62       can be supplied with -rb, otherwise they will be equal to those of  the
63       A topology.
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65       Starting  coordinates  can  be  read from trajectory with -t.  The last
66       frame with coordinates and velocities will be read,  unless  the  -time
67       option is used. Only if this information is absent will the coordinates
68       in the -c file be used.  Note that these velocities will  not  be  used
69       when  gen_vel  =  yes in your .mdp file. An energy file can be supplied
70       with -e to read Nose-Hoover  and/or  Parrinello-Rahman  coupling  vari‐
71       ables.
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73       gmx  grompp  can be used to restart simulations (preserving continuity)
74       by supplying just a checkpoint  file  with  -t.   However,  for  simply
75       changing the number of run steps to extend a run, using gmx convert-tpr
76       is more convenient than gmx grompp.  You then supply the old checkpoint
77       file  directly to gmx mdrun with -cpi. If you wish to change the ensem‐
78       ble or things like output frequency, then supplying the checkpoint file
79       to  gmx grompp with -t along with a new .mdp file with -f is the recom‐
80       mended procedure. Actually preserving the ensemble (if possible)  still
81       requires passing the checkpoint file to gmx mdrun -cpi.
82
83       By  default,  all bonded interactions which have constant energy due to
84       virtual site constructions will be removed. If this constant energy  is
85       not  zero,  this will result in a shift in the total energy. All bonded
86       interactions can be kept by turning  off  -rmvsbds.  Additionally,  all
87       constraints for distances which will be constant anyway because of vir‐
88       tual site constructions will be  removed.  If  any  constraints  remain
89       which involve virtual sites, a fatal error will result.
90
91       To  verify your run input file, please take note of all warnings on the
92       screen, and correct where necessary. Do also look at  the  contents  of
93       the  mdout.mdp  file; this contains comment lines, as well as the input
94       that gmx grompp has read. If in doubt, you can start  gmx  grompp  with
95       the -debug option which will give you more information in a file called
96       grompp.log (along with real debug info). You can see  the  contents  of
97       the  run input file with the gmx dump program. gmx check can be used to
98       compare the contents of two run input files.
99
100       The -maxwarn option can be used to override  warnings  printed  by  gmx
101       grompp  that  otherwise  halt output. In some cases, warnings are harm‐
102       less, but usually they are not. The user is advised to carefully inter‐
103       pret  the  output  messages  before attempting to bypass them with this
104       option.
105

OPTIONS

107       Options to specify input files:
108
109       -f [<.mdp>] (grompp.mdp)
110              grompp input file with MD parameters
111
112       -c [<.gro/.g96/…>] (conf.gro)
113              Structure file: gro g96 pdb brk ent esp tpr
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115       -r [<.gro/.g96/…>] (restraint.gro) (Optional)
116              Structure file: gro g96 pdb brk ent esp tpr
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118       -rb [<.gro/.g96/…>] (restraint.gro) (Optional)
119              Structure file: gro g96 pdb brk ent esp tpr
120
121       -n [<.ndx>] (index.ndx) (Optional)
122              Index file
123
124       -p [<.top>] (topol.top)
125              Topology file
126
127       -t [<.trr/.cpt/…>] (traj.trr) (Optional)
128              Full precision trajectory: trr cpt tng
129
130       -e [<.edr>] (ener.edr) (Optional)
131              Energy file
132
133       Options to specify input/output files:
134
135       -ref [<.trr/.cpt/…>] (rotref.trr) (Optional)
136              Full precision trajectory: trr cpt tng
137
138       Options to specify output files:
139
140       -po [<.mdp>] (mdout.mdp)
141              grompp input file with MD parameters
142
143       -pp [<.top>] (processed.top) (Optional)
144              Topology file
145
146       -o [<.tpr>] (topol.tpr)
147              Portable xdr run input file
148
149       -imd [<.gro>] (imdgroup.gro) (Optional)
150              Coordinate file in Gromos-87 format
151
152       Other options:
153
154       -[no]v (no)
155              Be loud and noisy
156
157       -time <real> (-1)
158              Take frame at or first after this time.
159
160       -[no]rmvsbds (yes)
161              Remove constant bonded interactions with virtual sites
162
163       -maxwarn <int> (0)
164              Number of allowed warnings during input processing. Not for nor‐
165              mal use and may generate unstable systems
166
167       -[no]zero (no)
168              Set  parameters for bonded interactions without defaults to zero
169              instead of generating an error
170
171       -[no]renum (yes)
172              Renumber atomtypes and minimize number of atomtypes
173

SEE ALSO

175       gmx(1)
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177       More    information    about    GROMACS    is    available    at     <‐
178       http://www.gromacs.org/>.
179
181       2019, GROMACS development team
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1862019.4                           Oct 02, 2019                    GMX-GROMPP(1)
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