Features & Capabilities

VOTCA is a tool to utilize automictically generated trajectories from LAMMPS or GROMACS to derive force fields for mesoscopic simulation at various levels of coarse graining. The VOTCA users have the capability to develop tailormade forcefield and efficiently scaleup their simulations.

Summary

Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a coarse-grained simulation package, which focuses on the analysis of molecular dynamics data and the development of systematic coarse-graining techniques. VOTCA allows the user to generate new potentials for mesoscopic simulations from atomistic molecular dynamics simulations. Trajectories will be analyzed to derive tabulated potentials consistent with the bead size of the mesoscopic simulation. A typical coarse-graining procedure includes sampling of the system of interest at the atomistic level, analysis of the trajectory using a specific mapping and a coarse-graining method to derive coarse-grained potentials and, in case of iterative methods, running coarse-grained simulations and iteratively refining the coarse-grained potentials. Two methods to generate the force fields are available in VOTCA:

• Iterative Boltzman inversion: structure-based approach aiming to reproduce distribution functions. It is an iterative method used to refine both bonded and non-bonded potentials.
• Force matching: aims to match the multibody potential of mean-force.

Two simulation engines for the atomistic simulations and the subsequent generation of the force field are supported by VOTCA in MAPS, GROMACS and LAMMPS. For each engine the corresponding atomistic trajectory should be supplied, i.e., it is not possible to run VOTCA with LAMMPS using a GROMACS trajectory and vice versa. The tabulated force fields generated by one engine are ready be used by the same engine in the subsequent mesoscale simulation.

References

1. Rühle et al. J. Chem. Theory Compu. 2009, 5(12), 3211-3223.