Auxiliary tools for automated atomistic and coarse-grained molecular dynamics simulations using GROMACS
Molecular dynamics simulations have complex workflows, including the generation of a model, setting up the environment, relaxation of the system and finally the production simulation. Despite the intrinsic complexity, the steps of the process are well-defined. For simulations of protein and/or DNA in solution, with or without ligand and with or without ions standard protocols are available. Gromit and martinate are versatile wrappers providing such protocols for atomistic (gromit) and coarse-grain (martinate) simulations, using the molecular simulation package Gromacs and, for martinate, the coarse grain Martini force field.