TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD

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.