Project ID: plumID:20.032
Name: Modeling the thermodynamics of conformational isomerism in solution via unsupervised clustering, the case of Sildenafil
Archive: https://github.com/mme-ucl/plumed-nest-data/raw/master/Clustering_Sildenafil.zip
Category: materials
Keywords: clustering, conformational isomers
PLUMED version: 2.4
Contributor: Matteo Salvalaglio
Submitted on: 17 Nov 2020
Publication: unpublished

PLUMED input files

File Compatible with
…Sildenafil/solids_setup/solid_analysis/plumed0.dat tested on v2.7 tested on master
…Sildenafil/solids_setup/solid_analysis/plumed1.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed10.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed11.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed12.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed13.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed14.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed15.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed16.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed17.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed18.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed19.dat tested on v2.7 tested on master
…Sildenafil/solids_setup/solid_analysis/plumed2.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed20.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed21.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed22.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed23.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed24.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed25.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed26.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed27.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed28.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed29.dat tested on v2.7 tested on master
…Sildenafil/solids_setup/solid_analysis/plumed3.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed30.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed31.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed32.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed33.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed34.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed35.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed36.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed37.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed38.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed39.dat tested on v2.7 tested on master
…Sildenafil/solids_setup/solid_analysis/plumed4.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed40.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed41.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed42.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed43.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed44.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed45.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed46.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed47.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed48.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed49.dat tested on v2.7 tested on master
…Sildenafil/solids_setup/solid_analysis/plumed5.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed50.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed51.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed52.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed53.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed54.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed55.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed56.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed57.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed58.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed59.dat tested on v2.7 tested on master
…Sildenafil/solids_setup/solid_analysis/plumed6.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed60.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed61.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed62.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed63.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed64.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed65.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed66.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed67.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed68.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed69.dat tested on v2.7 tested on master
…Sildenafil/solids_setup/solid_analysis/plumed7.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed70.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed71.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed72.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed73.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed74.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed75.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed76.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed77.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed78.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed79.dat tested on v2.7 tested on master
…Sildenafil/solids_setup/solid_analysis/plumed8.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed80.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed81.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed82.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed83.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed84.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed85.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed86.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed87.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed88.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed89.dat tested on v2.7 tested on master
…Sildenafil/solids_setup/solid_analysis/plumed9.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed90.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed91.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed92.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed93.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed94.dat tested on v2.7 tested on master
…ildenafil/solids_setup/solid_analysis/plumed95.dat tested on v2.7 tested on master
Clustering_Sildenafil/solvents_setup/plumed.dat tested on v2.7 tested on master
Clustering_Sildenafil/vacuum_setup/plumed.dat tested on v2.7 tested on master

Last tested: 25 Nov 2020, 11:44:29

Project description and instructions
Examples of plumed files used to compute and print to file the instantaneous value of the 6 dihedral dihedral angles defining the conformational state of sildenafil in vacuum, solution and in the crystal phase. In solution the slowest of the dihedral angles is biased. The angles are used to construct 1D FES and to perform unsupervised clustering to identify highly populated conformational states.

Submission history
[v1] 17 Nov 2020: original submission

Badge
Click on the image below and get the code to add the badge to your website!
plumeDnest:20.032