# 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.

#### [**Download Link**](http://digitalcommons.unl.edu/mechengfacpub/207/)

#### **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:](http://dx.doi.org/10.1038/s41598-017-06827-3)[10.1038/s41598-017-06827-3, open access](http://dx.doi.org/10.1038/s41598-017-06827-3)
- 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](http://www.sciencedirect.com/science/article/pii/S0045782514003880 "DOI:10.1016/j.cma.2014.10.018")