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>]] [-qmi [<.inp>]]
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).  Eventually  a  bi‐
27       nary  file is produced that can serve as the sole input file for the MD
28       program.
29
30       gmx grompp uses the atom names from the topology file. The  atom  names
31       in  the  coordinate file (option -c) are only read to generate warnings
32       when they do not match the atom names in the topology.  Note  that  the
33       atom names are irrelevant for the simulation as only the atom types are
34       used for generating interaction parameters.
35
36       gmx grompp uses a built-in preprocessor to  resolve  includes,  macros,
37       etc. The preprocessor supports the following keywords:
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39          #ifdef VARIABLE
40          #ifndef VARIABLE
41          #else
42          #endif
43          #define VARIABLE
44          #undef VARIABLE
45          #include "filename"
46          #include <filename>
47
48       The  functioning  of these statements in your topology may be modulated
49       by using the following two flags in your .mdp file:
50
51          define = -DVARIABLE1 -DVARIABLE2
52          include = -I/home/john/doe
53
54       For further information a C-programming  textbook  may  help  you  out.
55       Specifying  the -pp flag will get the pre-processed topology file writ‐
56       ten out so that you can verify its contents.
57
58       When using position restraints, a file with restraint coordinates  must
59       be supplied with -r (can be the same file as supplied for -c). For free
60       energy calculations, separate reference coordinates for the B  topology
61       can  be supplied with -rb, otherwise they will be equal to those of the
62       A topology.
63
64       Starting coordinates can be read from trajectory  with  -t.   The  last
65       frame  with  coordinates  and velocities will be read, unless the -time
66       option is used. Only if this information is absent will the coordinates
67       in  the  -c  file be used.  Note that these velocities will not be used
68       when gen_vel = yes in your .mdp file. An energy file  can  be  supplied
69       with  -e  to  read  Nose-Hoover and/or Parrinello-Rahman coupling vari‐
70       ables.
71
72       gmx grompp can be used to restart simulations  (preserving  continuity)
73       by  supplying  just  a  checkpoint  file  with -t.  However, for simply
74       changing the number of run steps to extend a run, using gmx convert-tpr
75       is more convenient than gmx grompp.  You then supply the old checkpoint
76       file directly to gmx mdrun with -cpi. If you wish to change the  ensem‐
77       ble or things like output frequency, then supplying the checkpoint file
78       to gmx grompp with -t along with a new .mdp file with -f is the  recom‐
79       mended  procedure. Actually preserving the ensemble (if possible) still
80       requires passing the checkpoint file to gmx mdrun -cpi.
81
82       By default, all bonded interactions which have constant energy  due  to
83       virtual  site constructions will be removed. If this constant energy is
84       not zero, this will result in a shift in the total energy.  All  bonded
85       interactions  can  be  kept  by turning off -rmvsbds. Additionally, all
86       constraints for distances which will be constant anyway because of vir‐
87       tual  site  constructions  will  be  removed. If any constraints remain
88       which involve virtual sites, a fatal error will result.
89
90       To verify your run input file, please take note of all warnings on  the
91       screen,  and  correct  where necessary. Do also look at the contents of
92       the mdout.mdp file; this contains comment lines, as well as  the  input
93       that  gmx  grompp  has read. If in doubt, you can start gmx grompp with
94       the -debug option which will give you more information in a file called
95       grompp.log  (along  with  real debug info). You can see the contents of
96       the run input file with the gmx dump program. gmx check can be used  to
97       compare the contents of two run input files.
98
99       The  -maxwarn  option  can  be used to override warnings printed by gmx
100       grompp that otherwise halt output. In some cases,  warnings  are  harm‐
101       less, but usually they are not. The user is advised to carefully inter‐
102       pret the output messages before attempting to bypass them with this op‐
103       tion.
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OPTIONS

106       Options to specify input files:
107
108       -f [<.mdp>] (grompp.mdp)
109              grompp input file with MD parameters
110
111       -c [<.gro/.g96/...>] (conf.gro)
112              Structure file: gro g96 pdb brk ent esp tpr
113
114       -r [<.gro/.g96/...>] (restraint.gro) (Optional)
115              Structure file: gro g96 pdb brk ent esp tpr
116
117       -rb [<.gro/.g96/...>] (restraint.gro) (Optional)
118              Structure file: gro g96 pdb brk ent esp tpr
119
120       -n [<.ndx>] (index.ndx) (Optional)
121              Index file
122
123       -p [<.top>] (topol.top)
124              Topology file
125
126       -t [<.trr/.cpt/...>] (traj.trr) (Optional)
127              Full precision trajectory: trr cpt tng
128
129       -e [<.edr>] (ener.edr) (Optional)
130              Energy file
131
132       -qmi [<.inp>] (topol-qmmm.inp) (Optional)
133              Input file for QM program
134
135       Options to specify input/output files:
136
137       -ref [<.trr/.cpt/...>] (rotref.trr) (Optional)
138              Full precision trajectory: trr cpt tng
139
140       Options to specify output files:
141
142       -po [<.mdp>] (mdout.mdp)
143              grompp input file with MD parameters
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145       -pp [<.top>] (processed.top) (Optional)
146              Topology file
147
148       -o [<.tpr>] (topol.tpr)
149              Portable xdr run input file
150
151       -imd [<.gro>] (imdgroup.gro) (Optional)
152              Coordinate file in Gromos-87 format
153
154       Other options:
155
156       -[no]v (no)
157              Be loud and noisy
158
159       -time <real> (-1)
160              Take frame at or first after this time.
161
162       -[no]rmvsbds (yes)
163              Remove constant bonded interactions with virtual sites
164
165       -maxwarn <int> (0)
166              Number of allowed warnings during input processing. Not for nor‐
167              mal use and may generate unstable systems
168
169       -[no]zero (no)
170              Set parameters for bonded interactions without defaults to  zero
171              instead of generating an error
172
173       -[no]renum (yes)
174              Renumber atomtypes and minimize number of atomtypes
175

SEE ALSO

177       gmx(1)
178
179       More     information    about    GROMACS    is    available    at    <‐
180       http://www.gromacs.org/>.
181
183       2022, GROMACS development team
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1882022.3                           Sep 02, 2022                    GMX-GROMPP(1)
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