1GMX-GROMPP(1) GROMACS GMX-GROMPP(1)
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6 gmx-grompp - Make a run input file
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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
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 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 gmx grompp uses a built-in preprocessor to resolve includes, macros,
37 etc. The preprocessor supports the following keywords:
38 #ifdef VARIABLE
40 #ifndef VARIABLE
41 #else
42 #endif
43 #define VARIABLE
44 #undef VARIABLE
45 #include "filename"
46 #include <filename>
47 The functioning of these statements in your topology may be modulated
49 by using the following two flags in your .mdp file:
50 define = -DVARIABLE1 -DVARIABLE2
52 include = -I/home/john/doe
53 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 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 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 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 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 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 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.
104
106 Options to specify input files:
107 -f [<.mdp>] (grompp.mdp)
109 grompp input file with MD parameters
110 -c [<.gro/.g96/...>] (conf.gro)
112 Structure file: gro g96 pdb brk ent esp tpr
113 -r [<.gro/.g96/...>] (restraint.gro) (Optional)
115 Structure file: gro g96 pdb brk ent esp tpr
116 -rb [<.gro/.g96/...>] (restraint.gro) (Optional)
118 Structure file: gro g96 pdb brk ent esp tpr
119 -n [<.ndx>] (index.ndx) (Optional)
121 Index file
122 -p [<.top>] (topol.top)
124 Topology file
125 -t [<.trr/.cpt/...>] (traj.trr) (Optional)
127 Full precision trajectory: trr cpt tng
128 -e [<.edr>] (ener.edr) (Optional)
130 Energy file
131 -qmi [<.inp>] (topol-qmmm.inp) (Optional)
133 Input file for QM program
134 Options to specify input/output files:
136 -ref [<.trr/.cpt/...>] (rotref.trr) (Optional)
138 Full precision trajectory: trr cpt tng
139 Options to specify output files:
141 -po [<.mdp>] (mdout.mdp)
143 grompp input file with MD parameters
144 -pp [<.top>] (processed.top) (Optional)
146 Topology file
147 -o [<.tpr>] (topol.tpr)
149 Portable xdr run input file
150 -imd [<.gro>] (imdgroup.gro) (Optional)
152 Coordinate file in Gromos-87 format
153 Other options:
155 -[no]v (no)
157 Be loud and noisy
158 -time <real> (-1)
160 Take frame at or first after this time.
161 -[no]rmvsbds (yes)
163 Remove constant bonded interactions with virtual sites
164 -maxwarn <int> (0)
166 Number of allowed warnings during input processing. Not for nor‐
167 mal use and may generate unstable systems
168 -[no]zero (no)
170 Set parameters for bonded interactions without defaults to zero
171 instead of generating an error
172 -[no]renum (yes)
174 Renumber atomtypes and minimize number of atomtypes
175
177 gmx(1)
178 More information about GROMACS is available at <‐
180 http://www.gromacs.org/>.
181
183 2022, GROMACS development team
1842022.3 Sep 02, 2022 GMX-GROMPP(1)