Project ID: plumID:19.046
Name: Optimal Collective from short simulations for Benzamidine-Trypsin ligand binding
Archive: https://gitlab.e-cam2020.eu/brotzakis/vac_metad_applications/raw/master/TRYPSIN/VAC_METAD_BENZAMIDINE_TRYPSIN.zip
Category: bio
Keywords: VAC-MetaD, optimised collective variables, binding free energy, unbinding rates, benzamidine trypsin, Structure Activity Relation
PLUMED version: 2.5-mod
Contributor: Faidon Brotzakis
Submitted on: 19 May 2019
Last revised: 20 May 2019
Publication: Z. F. Brotzakis, V. Limongelli, M. Parrinello, Accelerating the Calculation of Protein–Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables, Journal of Chemical Theory and Computation 15, 743–750 (2018)

PLUMED input files

File Compatible with
PLUMED_FM/plumed_FM.dat tested on v2.5 tested on master with custom code
PLUMED_VAC/plumed_VAC.dat tested on v2.5 tested on master with custom code
PLUMED_VAC_METAD/plumed_VAC_METAD.dat tested on v2.5 tested on master with custom code

Last tested: 18 Aug 2019, 14:16:09

Project description and instructions
The simulations have been carried out using GROMACS 5.1.4 and plumed v2.5. For detailed instructions, please visit this link. To obtaini the Funnel Metadynamics files, please contact Prof. Vittorio Limongelli (limonv_at_usi.ch). The VAC-MetaD cpp file is available at Isaac Yang Yi’s GitHub page.

Submission history
[v1] 19 May 2019: original submission
[v2] 20 May 2019: modified instructions and zip file

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plumeDnest:19.046