Josh V. Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, and Axel
Kohlmeyer.
TopoGromacs: Automated topology conversion from CHARMM to
GROMACS within VMD.
Journal of Chemical Information and Modeling, 56:1112-1116,
2016.
VERM2016B-ET
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 the
widely used molecular visualization and analysis software VMD. The
conversion process was diligently tested on a comprehensive set of biological
molecules in vacuo. The resulting comparison between energy terms shows
that the translation performed was lossless as the energies were unchanged
for identical starting configurations. By applying the conversion process to
conventional benchmark systems that mimic typical modestly sized MD
systems, we explore the effect of the implementation choices made in
CHARMM, NAMD, and GROMACS. The newly available automatic conversion
capability breaks down barriers between simulation tools and user
communities and allows users to easily compare simulation programs and
leverage their unique features without the tedium of constructing a topology
twice.
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