Molecular Energetics Group

Three main applications are in development at the Molecular Energetics group:

DLPGEN: This program creates input files for the MD packages DLPOLY and GROMACS. The main feature is the generation of molecular configurations with the molecules distributed as in crystal structures. This program is also able to prepare the input files to perform simulations using the two shell (Drude) models implemented in DLPOLY. Additionally, with the aid of ForConX, it is also possible to generate input files for CHARMM, LAMMPS, and AMBER. For more information click HERE.

AGGREGATES: This is a computer program that can be used to study the aggregation of molecules in molecular dynamic simulations results. Besides calculating several statistical properties relating the size distribution of the aggregates, the program is able to perform volumetric and shape analysis of the aggregates, compute Spatial Distribution Functions (SDF), Combined Distribution Functions (CDF), perform molecular conformation analysis and do a First Shell Analysis (FSA). It is currently designed to read trajectory files from DLPOLY, CHARMM, GROMACS, and LAMMPS, and it can also read PDB files. For more information click HERE.

STRFACT: This software computes total scattering factors of systems containing C, H, O, N, F, P, S, Cl, and Fe. The program can use trajectory data from DLPOLY, CHARMM, GROMACS, and LAMMPS. Furthermore, radial distribution functions can be computed and converted into scattering factors. For more information click HERE.