Published April 27, 2023 | Version v1

OpenMM simulations of DOPC using the CHARMM Drude2023 force field

Authors/Creators

  • 1. U.S. NIH, NHLBI Lab. of Membrane Biophysics

Description

The dataset contains a PSF, a formatted coordinate file (CRD), and DCD files with the final 200 ns from each of 3 replicate simulations from the paper

Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:
Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids

Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*
Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*
https://doi.org/10.1021/acs.jctc.3c00203


DCD file names indicate the lipid, replica number, and the time point of the final coordinate set in the file; each file has frames spaced at 10 ps over a 50 ns interval.

Notes

The data files contain additional atom types for the Drude particles and oxygen lone pairs

Files

Files (19.1 GB)

Name Size
md5:b3518a91d0a82524d54ebca909295b7e
1.6 GB Download
md5:1ad747372993ac07415a3d5ba3d0b14c
1.6 GB Download
md5:cc25eaa4a8730fd027a65f19941f3241
1.6 GB Download
md5:8b9de63f296f6d5e4a157b00869231da
1.6 GB Download
md5:8ab06b323fb70a63e2bd26e80195be1a
1.6 GB Download
md5:397e964d3ecf9efcec3b615ad6c8c6be
1.6 GB Download
md5:0caf92270e47613538a77d933d368dd4
1.6 GB Download
md5:f26eabf047a171e93fa5d2af2d70832a
1.6 GB Download
md5:b5974de4f07ddaadccbf98d242697ff9
1.6 GB Download
md5:0c25e348865d3cf6883853ad8083835d
1.6 GB Download
md5:82305589f58fa22eb74ac19a5eb55c21
1.6 GB Download
md5:72e0dea4f1f39dda22ca3fe212b1245e
3.7 MB Download
md5:f94b5786cdb2e402eace602e043352fc
1.6 GB Download
md5:e39b8ab062ef6da7d337cc0285d9ac03
6.5 MB Download

Additional details

Related works

Cites
Journal article: 10.1021/acs.jctc.3c00203 (DOI)