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 |   |
| plumed1.dat | |
| plumed2.dat | |
| plumed3.dat | |
| plumed4.dat | |
| plumed5.dat | |
| plumed6.dat | |
| plumed7.dat | |
| plumed8.dat | |
Last tested: 22 Apr 2024, 20:51:10
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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