Project ID: plumID:19.047
Name: Close Structure
Archive: https://archive.materialscloud.org/file/2019.0021/v2/close_structure.zip
Category: methods
Keywords: metadynamics, RMSD, path collective variables, property map
PLUMED version: 2.5
Contributor: Vojtech Spiwok
Submitted on: 22 May 2019
Last revised: 18 Jun 2019
Publication: J. Pazúriková, A. Křenek, V. Spiwok, M. Šimková, Reducing the number of mean-square deviation calculations with floating close structure in metadynamics, The Journal of Chemical Physics 146, 115101 (2017)

PLUMED input files

File Compatible with
cyclo/close/plumed_v2.dat tested on v2.6 tested on master
cyclo/normal/plumed_v2.dat tested on v2.6 tested on master
trpcage/close/plumed.dat tested on v2.6 tested on master
trpcage/normal/plumed.dat tested on v2.6 tested on master

Last tested: 15 Oct 2019, 20:04:36

Project description and instructions
Input files (input structures, topology, PLUMED input) for simulations used to demonstrate functionality of Close Structure algorithm (J. Chem. Phys. 2017, 146, 115101). The method replaces frequent calculations of root mean square deviations in Path collective variables or Property Map collective variables. This accelerates simulations. Input files for metadynamics simulation of cyclooctane derivative in vacuum and Trp-cage in implicit solvent with two or three, respectively, Isomap CVs (with and without Close Structure). Tested with OpenMPI4.0.0, Gromacs 2018.5 and PLUMED v2.5.0. Scripts provided

Submission history
[v1] 22 May 2019: original submission
[v2] 17 Jun 2019: update archive
[v3] 18 Jun 2019: switched to Materials Cloud

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plumeDnest:19.047