ProtoMD: A prototyping toolkit for multiscale molecular dynamics

Published: 1 May 2016| Version 1 | DOI: 10.17632/wrhg5n3wbt.1
Endre Somogyi, Andrew Abi Mansour, Peter J. Ortoleva


This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates ‘GROMACS wrapper’ to initiate MD simula... Title of program: ProtoMD Catalogue Id: AEZN_v1_0 Nature of problem Prototyping multiscale coarse-grained algorithms for molecular dynamics. Versions of this program held in the CPC repository in Mendeley Data AEZN_v1_0; ProtoMD; 10.1016/j.cpc.2016.01.014



Molecular Biology, Physical Chemistry, Molecular Physics, Statistical Physics, Biological Sciences, Computational Physics, Thermodynamics, Computational Method