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doi: 10.5281/zenodo.47649
The tar.gz archive contains simulation input files that were used in the publication Transmembrane potential modeling: Comparison between methods of constant electric field and ion imbalance. http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b01202 The files are meant to be used with Gromacs simulation package (gromacs.org). A modified Slipids force field, Slipids-VIS, is introduced. It uses Virtual Interaction sites in order to speed up simulation. The technique is described in the aforementioned work. The archive contains working topology for POPC lipid molecules and 6fs timestep without any significant loss of accuracy.
{"references": ["Josef Melcr, Daniel Bonhenry, \u0160t\u011bp\u00e1n Timr, and Pavel Jungwirth, Journal of Chemical Theory and Computation Article ASAP, DOI: 10.1021/acs.jctc.5b01202", "J\u00e4mbeck, J. P. M.; Lyubartsev, A. P. J. Chem. Theory Comput.2012 , 8 , 2938-2948.", "J\u00e4mbeck, J. P. M.; Lyubartsev, A. P. J. Phys. Chem. B 2012 , 116 , 3164-3179."]}
Slipids, Slipids-VIS, MD simulation, Gromacs topology, Virtual interaction sites
Slipids, Slipids-VIS, MD simulation, Gromacs topology, Virtual interaction sites
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