Recommended Software Tools¶
The listed programs are used in this manual and are generally considered necessary.
Packmol is a free molecule packing tool (written in Fortran), created by José Mario Martínez, a professor of mathematics at the State University of Campinas, Brazil. Packmol allows a specified number of molecules to be packed at defined separating distances within a certain region of space. More information regarding downloading and installing Packmol is available on their homepage:
One of Packmol’s limitations is that it is unaware of topology; it treats each molecule or group of molecules as a rigid set of points. It is highly suggested to used the optimized structure of the molecule as the input file to packmol.
Another more serious limitation is that it is not aware of periodic boundary conditions (PBC). As a result, when using Packmol to pack PDBs for GOMC, it is recommended to pack to a box 1 Angstroms smaller than the simulation box size. This prevents hard overlaps over the periodic boundary.
VMD (Visual Molecular Dynamics) is a 3-D visualization and manipulation engine for molecular systems written in C-language. VMD is distributed and maintained by the University of Illinois at Urbana-Champaign. Its sources and binaries are free to download. It comes with a robust scripting engine, which is capable of running python and tcl scripts. More info can be found here:
Although GOMC uses the same fundamental file types, PDB (coordinates) and PSF (topology) as VMD, it uses some special tricks to obey certain rules of those file formats. One useful purpose of VMD is visualization and analyze your systems.
Nonetheless, the most critical part of VMD is a tool called PSFGen. PSFGen uses a tcl or python script to generate a PDB and PSF file for a system of one or more molecules. It is, perhaps, the most convenient way to generate a compliant PSF file.
To read more about PSFGen, reference: