GROMACS

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GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

How to submit calculations

Gromacs is installed in Kimik, currently you should use more than one node.

qs 2 l grom script

Where the script file should contain something like script_gromacs

Gromacs file types:

Molecular Topology file (.top) The molecular topology file is generated by the program pdb2gmx. pdb2gmx translates a pdb structure file of any peptide or protein to a molecular topology file. This topology file contains a complete description of all the interactions in your peptide or protein.

Molecular Structure file (.gro, .pdb) When the pdb2gmx program is executed to generate a molecular topology, it also translates the structure file (.pdb file) to a gromos structure file (.gro file). The main difference between a pdb file and a gromos file is their format and that a .gro file can also hold velocities. However, if you do not need the velocities, you can also use a pdb file in all programs. To generate a box of solvent molecules around the peptide, the program genbox is used. First the program editconf should be used to define a box of appropriate size around the molecule. genbox dissolves a solute molecule (the peptide) into any solvent (in this case water). The output of genbox is a gromos structure file of the peptide dissolved in water. The genbox program also changes the molecular topology file (generated by pdb2gmx) to add solvent to the topology.

Molecular Dynamics parameter file (.mdp) The Molecular Dynamics Parameter (.mdp) file contains all information about the Molecular Dynamics simulation itself e.g. time-step, number of steps, temperature, pressure etc. The easiest way of handling such a file is by adapting a sample .mdp file.

Index file (.ndx) Sometimes you may need an index file to specify actions on groups of atoms (e.g. Temperature coupling, accelerations, freezing). Usually the default index groups will be sufficient.

Run input file (.tpr) The next step is to combine the molecular structure (.gro file), topology (.top file) MD-parameters (.mdp file) and (optionally) the index file (ndx) to generate a run input file (.tpr extension or .tpb if you don't have XDR). This file contains all information needed to start a simulation with GROMACS. The grompp program processes all input files and generates the run input .tpr file.

Trajectory file (.trr) Once the run input file is available, we can start the simulation. The program which starts the simulation is called mdrun. The only input file of mdrun you usually need to start a run is the run input file (.tpr file). The output files of mdrun are the trajectory file (.trr file or .trj if you don't have XDR) and a logfile ( .log file).

GROMACS associated programs

Programs for input preparation:

pdb2gmx

editconf

genbox

Program to run the energy minimizations and molecular dinamics. It must only be used through the queue system, use the commands and the script files as detailed above.

mdrun

Links

http://www.gromacs.org/

Getting started: http://manual.gromacs.org/current/online/getting_started.html

Chart: http://manual.gromacs.org/current/online/flow.html

Manual

Online Manual (quite useful): http://manual.gromacs.org/current/

Manual of the 3.2 version is available on the bookshelf and here.[1]

Tutorial

https://distributedscience.wordpress.com/2019/11/10/tutorial-modelling-post-translational-modified-proteins-with-gromacs/