TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

ABSTRACT: Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within

SUBMITTER: Vermaas JV 

PROVIDER: S-EPMC5543333 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature