A tool for simplified and automatized usage of the GROMACS package

Abstract:

Nowadays, the scientific application of informatics in molecular biology becomes a useful tool. A major drawback, however, is the fact that many in silico techniques are still approachable only for experts in this particular field. One such method, called molecular dynamics (MD), is a complex simulation of movement of all atoms in a selected system. This method is widely applied in cases when experimental approach fails to deliver information one is looking for. Due to its undeniable advantages, MD is especially popular in structural research. In contrast to experimental methods, it provides insight into atomic-scale interactions, yielding information that differs from that obtained by laboratory methods. In this work we present a tool for simplified and automated generation of the MD simulations with GROMACS package.