Published March 25, 2016
| Version v1
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Simulation files for POPC lipid membrane with Slipids-VIS force field for Gromacs MD simulation engine
Creators
- 1. Institute of Organic Chemistry and Biochemistry CAS, v.v.i., Czech Republic.
Description
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.
Files
Files
(497.2 kB)
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md5:4d248df92038946291437f87d95c6b61
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497.2 kB | Download |
Additional details
Related works
- Is cited by
- 10.1021/acs.jctc.5b01202 (DOI)
References
- Josef Melcr, Daniel Bonhenry, Štěpán Timr, and Pavel Jungwirth, Journal of Chemical Theory and Computation Article ASAP, DOI: 10.1021/acs.jctc.5b01202
- Jämbeck, J. P. M.; Lyubartsev, A. P. J. Chem. Theory Comput.2012 , 8 , 2938-2948.
- Jämbeck, J. P. M.; Lyubartsev, A. P. J. Phys. Chem. B 2012 , 116 , 3164-3179.