Published May 9, 2023 | Version v1
Dataset Open

OpenMM simulations of POPE 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.7872447 have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.

Files

Files (6.5 GB)

Name Size Download all
md5:23e0b2bcebb322daba0781aafe34c542
2.2 GB Download
md5:367cb18c4ea179a10bbd03bdb96d8ab8
2.2 GB Download
md5:75514cc4e031ced204372e43a49555fa
2.2 GB Download
md5:dec4cd8503ed9aa56293c449f65776a6
3.5 MB Download
md5:517e6e61475a6abf3e2c620dd2a8a07d
6.0 MB Download