MOLECULAR DYNAMICS SIMULATION TOOLBOX

Source: https://jerugroup.eng.ox.ac.uk/software/molecular-dynamics-simulation-toolbox Parent: https://jerugroup.eng.ox.ac.uk/software

MOLECULAR DYNAMICS SIMULATION TOOLBOX

This software was developed, and is provided under a general use license, to calculate the continuum-like deformation gradient and internal stress for any particle group in an MD simulation that uses CHARMM force fields. This software can also calculate the continuum-like interaction stress applied by one group of particles on any other group.

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Relevant publications

• L. Zhang, Z. Zhang, J. Jasa, D. Li, R. Cleveland, M. Negahban and A. Jérusalem. Molecular dynamics simulations of heterogeneous cell membranes in response to uniaxial membrane stretches at high loading rates. Scientific Reports, 7(8316):1-12, 2017.DOI:10.1038/s41598-017-06827-3, open access
• L. Zhang, J. Jasa, G. Gazonas, A. Jérusalem and M. Negahban. Extracting continuum-like deformation and stress from Molecular Dynamics simulations. Computer Methods in Applied Mechanics and Engineering, 283:1010-1031, 2015.DOI:10.1371/journal.pone.0116532