Exporting potentials: GROMACS

Preparing a set of files for MD simulation with GROMACS is quite a challenge even for an experienced user. MagicTools provides few exporting procedures which hopefully make your life a bit easier. GROMACS requires provide five files: starting geometry (http://manual.gromacs.org/current/online/gro.html.gro, .pdb) and http://www.gromacs.org/Documentation/File_Formats/Index_Fileindex file (.ndx), http://www.gromacs.org/Documentation/File_Formats/Topology_Filetopology file (.top), http://www.gromacs.org/Documentation/File_Formats/.mdp_Filesimulation parameters (.mdp) and tabulated potentials (.xvg)

[xmol2gro]xmol2gro - converts .xmol structure file into GROMACS supported .gro format. Another workaround is to use VMD for opening .xmol and saving it in .pdb format. Once the starting structure is prepared, the index file can be generated by make_ndx tool, which is a part of GROMACS. Note that you shall create an individual group in the index file for every bead/atom type present in the system.
[GromacsTopology]GromacsTopology - a simple tool to create a topology file, having the same interactions as in MagiC. Note that you shall manually state the actual number of molecules to be present in the system in the generated .top file.
[PotsExport2Gromacs]PotsExport2Gromacs exports the list of potentials to a GROMACS's .xvg tabulated potential format, and also generates strings energygrps and energygrp_table, which shall be stated in .mdp file.

We highly recommend to check http://www.gromacs.org/Documentation/How-tos/Tabulated_PotentialsHowTo Tabulated potentials and respective part of the MagiC tutorial for getting some practical experience of the potential exporting procedure.