title: 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 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.
authors.affiliation: Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.|Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.|Beckman Insitute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Josh V
authors.initials: JV
authors.lastname: Vermaas
authors.affiliation: Beckman Insitute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: David J
authors.initials: DJ
authors.lastname: Hardy
authors.affiliation: Beckman Insitute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: John E
authors.initials: JE
authors.lastname: Stone
authors.affiliation: Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.|Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.|Beckman Insitute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.
authors.forename: Emad
authors.initials: E
authors.lastname: Tajkhorshid
authors.affiliation: Insitute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States.
authors.forename: Axel
authors.initials: A
authors.lastname: Kohlmeyer
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D001331:Automation; D002241:Carbohydrates / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D016247:Information Storage and Retrieval / Q000379:methods*; D008055:Lipids / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012984:Software
chemical_list: D000596:Amino Acids; D002241:Carbohydrates; D008055:Lipids; D009842:Oligopeptides; D012313:RNA; D004247:DNA