Project ID: plumID:19.077
Name: Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from MD Simulations
Archive: https://archive.materialscloud.org/record/file?file_id=5ea5798d-66e8-4309-8785-1e47ce8758d4&record_id=385&filename=TBP.zip
Category: materials
Keywords: metadynamics, peptide-surface binding
PLUMED version: 2.4
Contributor: Jim Pfaendtner
Submitted on: 24 Oct 2019
Last revised: 23 May 2020
Publication: J. Sampath, A. Kullman, R. Gebhart, G. Drobny, J. Pfaendtner, Molecular recognition and specificity of biomolecules to titanium dioxide from molecular dynamics simulations, npj Computational Materials 6 (2020)

PLUMED input files

File Compatible with
TBP/12mer_NH.dat tested on v2.7 tested on master
TBP/12mer_NeNH.dat tested on v2.7 tested on master
TBP/6mer_NH.dat tested on v2.7 tested on master
TBP/6mer_NeNH.dat tested on v2.7 tested on master
TBP/ARG_NH.dat tested on v2.7 tested on master
TBP/ARG_NNH.dat tested on v2.7 tested on master
TBP/ARG_NeH.dat tested on v2.7 tested on master
TBP/ARG_NeNH.dat tested on v2.7 tested on master
TBP/ASP_NH.dat tested on v2.7 tested on master
TBP/ASP_NNH.dat tested on v2.7 tested on master
TBP/ASP_NeH.dat tested on v2.7 tested on master
TBP/ASP_NeNH.dat tested on v2.7 tested on master
TBP/LYS_NH.dat tested on v2.7 tested on master
TBP/LYS_NNH.dat tested on v2.7 tested on master
TBP/LYS_NeH.dat tested on v2.7 tested on master
TBP/LYS_NeNH.dat tested on v2.7 tested on master

Last tested: 22 Jul 2021, 09:20:14

Project description and instructions
The input files can be used to generate free energy profiles in the manuscript, using “sum_hills –hills *.HILLS –idw d1.z –kt 2.5 –mintozero”. GROMACS 5.1.2 package was used for MD simulations.

Submission history
[v1] 24 Oct 2019: original submission
[v2] 23 May 2020: updated doi

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plumeDnest:19.077