Project ID: plumID:22.044
Name: Colloid Crystallisation Analyses
Archive: https://github.com/aaronrfinney/VAMP-MSM/raw/main/PLUMED-driver.zip
Category: materials
Keywords: Q4, Q6, Pair Entropy, DFS
PLUMED version: 2.7.2
Contributor: Aaron Finney
Submitted on: 21 Dec 2022
Publication: A. R. Finney, M. Salvalaglio, A variational approach to assess reaction coordinates for two-step crystallization. The Journal of Chemical Physics. 158 (2023)

PLUMED input files

File Compatible with
plumed-all-search.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:48:19

Project description and instructions
The input file is designed to be executed using the driver to post-process LAMMPS simulation trajectories and compute a range of CVs used in Variational Analysis of Markov Processes (VAMP) and to construct Bayesian Markov State Models (MSMs). Run the driver using e.g. plumed driver --ixyz dump.3Dcolloid.xyz --plumed plumed-all-search.dat --timestep 1 --trajectory-stride 1 --box 92.83178,92.83178,92.83178.

Submission history
[v1] 21 Dec 2022: original submission

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plumeDnest:22.044