Project ID: plumID:21.048
Name: Enhancing ligand exploration within a channel pore and fenestrations using metadynamics
Archive: https://github.com/etaoster/etaoster.github.io/raw/main/fenestration_project/plumed_wtmetad.zip
Category: bio
Keywords: well-tempered metadynamics, protein-ligand enhanced sampling, sodium channel, Nav, small molecule drug
PLUMED version: 2.5
Contributor: Elaine Tao
Submitted on: 30 Nov 2021
Last revised: 25 Jan 2022
Publication: E. Tao, B. Corry, Characterizing fenestration size in sodium channel subtypes and their accessibility to inhibitors. Biophysical Journal. 121, 193–206 (2022)

PLUMED input files

File Compatible with
plumed0.dat tested on v2.8 tested on master
plumed1.dat tested on v2.8 tested on master
plumed2.dat tested on v2.8 tested on master
plumed3.dat tested on v2.8 tested on master
plumed4.dat tested on v2.8 tested on master
plumed5.dat tested on v2.8 tested on master
plumed6.dat tested on v2.8 tested on master
plumed7.dat tested on v2.8 tested on master
plumed8.dat tested on v2.8 tested on master

Last tested: 19 Nov 2022, 10:51:09

Project description and instructions
Files are for running nine different walkers using AMBER/20 patched with PLUMED/2.5.0 on separate GPUs. Metadynamics potential is applied to the ligand (center of mass) position relative to the protein defined by three collective variables (z, r and theta).

Submission history
[v1] 30 Nov 2021: original submission
[v2] 25 Jan 2022: updated doi

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plumeDnest:21.048