1grompp(1) GROMACS suite, VERSION 4.5 grompp(1)
2
6 grompp - makes a run input file
7 VERSION 4.5
9
11 grompp -f grompp.mdp -po mdout.mdp -c conf.gro -r conf.gro -rb conf.gro
12 -n index.ndx -p topol.top -pp processed.top -o topol.tpr -t traj.trr -e
13 ener.edr -[no]h -[no]version -nice int -[no]v -time real -[no]rmvsbds
14 -maxwarn int -[no]zero -[no]renum
15
17 The gromacs preprocessor reads a molecular topology file, checks the
18 validity of the file, expands the topology from a molecular description
19 to an atomic description. The topology file contains information about
20 molecule types and the number of molecules, the preprocessor copies
21 each molecule as needed. There is no limitation on the number of mole‐
22 cule types. Bonds and bond-angles can be converted into constraints,
23 separately for hydrogens and heavy atoms. Then a coordinate file is
24 read and velocities can be generated from a Maxwellian distribution if
25 requested. grompp also reads parameters for the mdrun (eg. number of
26 MD steps, time step, cut-off), and others such as NEMD parameters,
27 which are corrected so that the net acceleration is zero. Eventually a
28 binary file is produced that can serve as the sole input file for the
29 MD program.
30 grompp uses the atom names from the topology file. The atom names in
33 the coordinate file (option -c) are only read to generate warnings
34 when they do not match the atom names in the topology. Note that the
35 atom names are irrelevant for the simulation as only the atom types are
36 used for generating interaction parameters.
37 grompp uses a built-in preprocessor to resolve includes, macros
40 etcetera. The preprocessor supports the following keywords:
41 ifdef VARIABLE
43 ifndef VARIABLE
45 else
47 endif
49 define VARIABLE
51 undef VARIABLE include "filename"
53 include filename
55 The functioning of these statements in your topology may be modulated
57 by using the following two flags in your mdp file:
58 define = -DVARIABLE1 -DVARIABLE2
60 include = /home/john/doe
62 For further information a C-programming textbook may help you out.
64 Specifying the -pp flag will get the pre-processed topology file writ‐
65 ten out so that you can verify its contents.
66 If your system does not have a c-preprocessor, you can still use
69 grompp, but you do not have access to the features from the cpp. Com‐
70 mand line options to the c-preprocessor can be given in the .mdp file.
71 See your local manual (man cpp).
72 When using position restraints a file with restraint coordinates can be
75 supplied with -r, otherwise restraining will be done with respect to
76 the conformation from the -c option. For free energy calculation the
77 the coordinates for the B topology can be supplied with -rb, otherwise
78 they will be equal to those of the A topology.
79 Starting coordinates can be read from trajectory with -t. The last
82 frame with coordinates and velocities will be read, unless the -time
83 option is used. Note that these velocities will not be used when
84 gen_vel = yes in your .mdp file. An energy file can be supplied with
85 -e to read Nose-Hoover and/or Parrinello-Rahman coupling variables.
86 Note that for continuation it is better and easier to supply a check‐
87 point file directly to mdrun, since that always contains the complete
88 state of the system and you don't need to generate a new run input
89 file. Note that if you only want to change the number of run steps tpb‐
90 conv is more convenient than grompp.
91 Using the -morse option grompp can convert the harmonic bonds in your
94 topology to morse potentials. This makes it possible to break bonds.
95 For this option to work you need an extra file in your $GMXLIB with
96 dissociation energy. Use the -debug option to get more information on
97 the workings of this option (look for MORSE in the grompp.log file
98 using less or something like that).
99 By default all bonded interactions which have constant energy due to
102 virtual site constructions will be removed. If this constant energy is
103 not zero, this will result in a shift in the total energy. All bonded
104 interactions can be kept by turning off -rmvsbds. Additionally, all
105 constraints for distances which will be constant anyway because of vir‐
106 tual site constructions will be removed. If any constraints remain
107 which involve virtual sites, a fatal error will result.
108 To verify your run input file, please make notice of all warnings on
110 the screen, and correct where necessary. Do also look at the contents
111 of the mdout.mdp file, this contains comment lines, as well as the
112 input that grompp has read. If in doubt you can start grompp with the
113 -debug option which will give you more information in a file called
114 grompp.log (along with real debug info). Finally, you can see the con‐
115 tents of the run input file with the gmxdump program.
116
118 -f grompp.mdp Input, Opt.
119 grompp input file with MD parameters
120 -po mdout.mdp Output
122 grompp input file with MD parameters
123 -c conf.gro Input
125 Structure file: gro g96 pdb tpr etc.
126 -r conf.gro Input, Opt.
128 Structure file: gro g96 pdb tpr etc.
129 -rb conf.gro Input, Opt.
131 Structure file: gro g96 pdb tpr etc.
132 -n index.ndx Input, Opt.
134 Index file
135 -p topol.top Input
137 Topology file
138 -pp processed.top Output, Opt.
140 Topology file
141 -o topol.tpr Output
143 Run input file: tpr tpb tpa
144 -t traj.trr Input, Opt.
146 Full precision trajectory: trr trj cpt
147 -e ener.edr Input, Opt.
149 Energy file
150
153 -[no]hno
154 Print help info and quit
155 -[no]versionno
157 Print version info and quit
158 -nice int 0
160 Set the nicelevel
161 -[no]vno
163 Be loud and noisy
164 -time real -1
166 Take frame at or first after this time.
167 -[no]rmvsbdsyes
169 Remove constant bonded interactions with virtual sites
170 -maxwarn int 0
172 Number of allowed warnings during input processing
173 -[no]zerono
175 Set parameters for bonded interactions without defaults to zero
176 instead of generating an error
177 -[no]renumyes
179 Renumber atomtypes and minimize number of atomtypes
180
183 gromacs(7)
184 More information about GROMACS is available at <http://www.gro‐
186 macs.org/>.
187 Thu 26 Aug 2010 grompp(1)