title: PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories.
abstract: Development of coarse-grained (CG) molecular dynamics models is often a laborious process which commonly relies upon approximations to similar models, rather than systematic parametrization. PyCGTOOL automates much of the construction of CG models via calculation of both equilibrium values and force constants of internal coordinates directly from atomistic molecular dynamics simulation trajectories. The derivation of bespoke parameters from atomistic simulations improves the quality of the CG model compared to the use of generic parameters derived from other molecules, while automation greatly reduces the time required. The ease of configuration of PyCGTOOL enables the rapid investigation of multiple atom-to-bead mappings and topologies. Although we present PyCGTOOL used in combination with the GROMACS molecular dynamics engine its use of standard trajectory input libraries means that it is in principle compatible with other software. The software is available from the URL https://github.com/jag1g13/pycgtool as the following doi: 10.5281/zenodo.259330 .
authors.affiliation: School of Chemistry, University of Southampton , Hampshire, SO17 1BJ, United Kingdom.
authors.forename: James A
authors.initials: JA
authors.lastname: Graham
authors.affiliation: School of Chemistry, University of Southampton , Hampshire, SO17 1BJ, United Kingdom.
authors.forename: Jonathan W
authors.identifier: 0000-0003-2639-2746
authors.initials: JW
authors.lastname: Essex
authors.affiliation: School of Chemistry, University of Southampton , Hampshire, SO17 1BJ, United Kingdom.
authors.forename: Syma
authors.identifier: 0000-0002-3694-5044
authors.initials: S
authors.lastname: Khalid
mesh_terms: D001331:Automation; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation