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.

Figure 1

Schematic comparison of the input file formats and procedures needed to run a simulation using CHARMM/NAMD (left) or GROMACS (right). Arrows indicate the flow of information during conversion processes and are labeled according to the tool that carries out the process. The conversion process highlighted here is shown as a black arrow and labeled in black, while the existing tools and methods are gray. The border on the GROMACS side indicates the border of the three distinct files needed by grompp to generate a binary run ( .tpr) file.

Figure 2

Energy difference of each potential energy term for tripeptide systems computed by NAMD, CHARMM, and GROMACS. The lowest line in each bar indicates the maximum energy difference observed in all 8,000 tripeptides, the highest line the minimum energy difference observed, and the middle line the mean energy difference.