Project ID: plumID:21.000
Name: Uremic toxin time scale dynamics
Archive: https://github.com/UWPRG/pbut_tica-msm/raw/master/plumed-nest.zip
Category: bio
Keywords: uremic toxin, serum albumin, Time-structure Independent Components Analysis (tICA), Markov state models (MSMs)
PLUMED version: 2.4
Contributor: Jim Pfaendtner
Submitted on: 04 Jan 2021
Last revised: 04 Jun 2021
Publication: J. Ludwig, J. Smith, J. Pfaendtner, Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum Albumin, The Journal of Physical Chemistry B 125, 2910–2920 (2021)

PLUMED input files

File Compatible with
plumed.dat tested on v2.7 tested on master

Last tested: 22 Jul 2021, 09:06:17

Project description and instructions
Basic plumed files used to determine residues key to the bound poses of uremic toxins in HSA’s Sudlow site ii. Plumed files are used to analyze GROMACS (2016) trajectories.

Submission history
[v1] 04 Jan 2021: original submission
[v2] 04 Jun 2021: updated doi

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plumeDnest:21.000