Published May 13, 2023 | Version v1

OpenMM simulations of DLPC using the CHARMM Drude2023 force field in xtc format

Authors/Creators

Description

The dataset contains a PSF, a formatted coordinate file (CRD), and XTC 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

XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.

The DCD sub-files in 10.5281/zenodo.7872783 have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.

Files

Files (5.8 GB)

Name Size
md5:d12c4be3dd869b22e8e749a6b2ea7bad
5.4 MB Download
md5:13d0e8b61cfd8fa20568ee3a579a19dd
1.9 GB Download
md5:5f0c099428e5be5a9f0186d2ae19f083
1.9 GB Download
md5:5b2dfce94d087566f5049c206c8783ea
1.9 GB Download
md5:a4823d705eee1e85ba5373453fd87f4a
3.1 MB Download