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>]]
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]
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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 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.
36 gmx grompp uses a built-in preprocessor to resolve includes, macros,
38 etc. The preprocessor supports the following keywords:
39 #ifdef VARIABLE
41 #ifndef VARIABLE
42 #else
43 #endif
44 #define VARIABLE
45 #undef VARIABLE
46 #include "filename"
47 #include <filename>
48 The functioning of these statements in your topology may be modulated
50 by using the following two flags in your .mdp file:
51 define = -DVARIABLE1 -DVARIABLE2
53 include = -I/home/john/doe
54 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 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.
64 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.
72 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 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 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 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
107 Options to specify input files:
108 -f [<.mdp>] (grompp.mdp)
110 grompp input file with MD parameters
111 -c [<.gro/.g96/…>] (conf.gro)
113 Structure file: gro g96 pdb brk ent esp tpr
114 -r [<.gro/.g96/…>] (restraint.gro) (Optional)
116 Structure file: gro g96 pdb brk ent esp tpr
117 -rb [<.gro/.g96/…>] (restraint.gro) (Optional)
119 Structure file: gro g96 pdb brk ent esp tpr
120 -n [<.ndx>] (index.ndx) (Optional)
122 Index file
123 -p [<.top>] (topol.top)
125 Topology file
126 -t [<.trr/.cpt/…>] (traj.trr) (Optional)
128 Full precision trajectory: trr cpt tng
129 -e [<.edr>] (ener.edr) (Optional)
131 Energy file
132 Options to specify input/output files:
134 -ref [<.trr/.cpt/…>] (rotref.trr) (Optional)
136 Full precision trajectory: trr cpt tng
137 Options to specify output files:
139 -po [<.mdp>] (mdout.mdp)
141 grompp input file with MD parameters
142 -pp [<.top>] (processed.top) (Optional)
144 Topology file
145 -o [<.tpr>] (topol.tpr)
147 Portable xdr run input file
148 -imd [<.gro>] (imdgroup.gro) (Optional)
150 Coordinate file in Gromos-87 format
151 Other options:
153 -[no]v (no)
155 Be loud and noisy
156 -time <real> (-1)
158 Take frame at or first after this time.
159 -[no]rmvsbds (yes)
161 Remove constant bonded interactions with virtual sites
162 -maxwarn <int> (0)
164 Number of allowed warnings during input processing. Not for nor‐
165 mal use and may generate unstable systems
166 -[no]zero (no)
168 Set parameters for bonded interactions without defaults to zero
169 instead of generating an error
170 -[no]renum (yes)
172 Renumber atomtypes and minimize number of atomtypes
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175 gmx(1)
176 More information about GROMACS is available at <‐
178 http://www.gromacs.org/>.
179
181 2019, GROMACS development team
1822019.4 Oct 02, 2019 GMX-GROMPP(1)