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gromppMain Table of Contents |
VERSION 3.3.1
Thu 11 May 2006
| VERSION 3.3.1 |
The gromacs preprocessor reads a molecular topology file, checks the validity of the file, expands the topology from a molecular description to an atomic description. The topology file contains information about molecule types and the number of molecules, the preprocessor copies each molecule as needed. There is no limitation on the number of molecule types. Bonds and bond-angles can be converted into constraints, separately for hydrogens and heavy atoms. Then a coordinate file is read and velocities can be generated from a Maxwellian distribution if requested. grompp also reads parameters for the mdrun (eg. number of MD steps, time step, cut-off), and others such as NEMD parameters, which are corrected so that the net acceleration is zero. Eventually a binary file is produced that can serve as the sole input file for the MD program.
grompp uses the atom names from the topology file. The atom names in the coordinate file (option -c) are only read to generate warnings when they do not match the atom names in the topology. Note that the atom names are irrelevant for the simulation as only the atom types are used for generating interaction parameters.
grompp calls a preprocessor to resolve includes, macros etcetera. By default we use the cpp in your path. To specify a different macro-preprocessor (e.g. m4) or alternative location you can put a line in your parameter file specifying the path to that program. Specifying -pp will get the pre-processed topology file written out.
If your system does not have a c-preprocessor, you can still use grompp, but you do not have access to the features from the cpp. Command line options to the c-preprocessor can be given in the .mdp file. See your local manual (man cpp).
When using position restraints a file with restraint coordinates can be supplied with -r, otherwise restraining will be done with respect to the conformation from the -c option. For free energy calculation the the coordinates for the B topology can be supplied with -rb, otherwise they will be equal to those of the A topology.
Starting coordinates can be read from trajectory with -t. The last frame with coordinates and velocities will be read, unless the -time option is used. Note that these velocities will not be used when gen_vel = yes in your .mdp file. An energy file can be supplied with -e to have exact restarts when using pressure and/or Nose-Hoover temperature coupling. For an exact restart do not forget to turn off velocity generation and turn on unconstrained starting when constraints are present in the system. If you want to continue a crashed run, it is easier to use tpbconv.
When preparing an input file for parallel mdrun it may be advantageous to partition the simulation system over the nodes in a way in which each node has a similar amount of work. The -shuffle option does just that. For a single protein in water this does not make a difference, however for a system where you have many copies of different molecules (e.g. liquid mixture or membrane/water system) the option is definitely a must. The output trajectories will also be shuffled. grompp writes an index file (option -deshuf) which can be used with trjconv to deshuffle the trajectories.
A further optimization for parallel systems is the -sort option which sorts molecules according to coordinates. This must always be used in conjunction with -shuffle, however sorting also works when you have only one molecule type.
Using the -morse option grompp can convert the harmonic bonds in your topology to morse potentials. This makes it possible to break bonds. For this option to work you need an extra file in your $GMXLIB with dissociation energy. Use the -debug option to get more information on the workings of this option (look for MORSE in the grompp.log file using less or something like that).
By default all bonded interactions which have constant energy due to virtual site constructions will be removed. If this constant energy is not zero, this will result in a shift in the total energy. All bonded interactions can be kept by ringany number of decimal places, the format will then be n+5 positions with n decimal places (n+1 for velocities) in stead of 8 with 3 (with 4 for velocities). Upon reading, the precision will be inferred from the distance between the decimal points (which will be n+5). Columns contain the following information (from left to right):
| Main Table of Contents | VERSION 3.2 |
| GROMACS homepage | Sun 25 Jan 2004 |
% gmxdump -s topol.tpaor if you're not such a fast reader:
% gmxdump -s topol.tpa | more
You can also compare two tpa files using:
% gmxcheck -s1 top1 -s2 top2 | more
| Main Table of Contents | VERSION 3.1 |
| GROMACS homepage | Sun 25 Jan 2004 |
| Main Table of Contents | VERSION 3.2 |
| GROMACS homepage | Sun 25 Jan 2004 |
TITLE x(i) (10f8.3) box(m) (10f8.8)The number of atoms is not stored, neither is there any indication of whether a box is present. The box is stored only for constant pressure simulations. So, you simply have to remember this stuff.
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