Project ID: plumID:20.005
Name: Muscarinic M2 receptor/ligand Frequency-Adaptive Metadynamics and QM/MM calculations
Category: bio
Keywords: Frequency-adaptive metadynamics, multiple-walkers metadynamics, well-tempered metadynamics, GPCR, receptor, Adiabatic Bias MD
PLUMED version: 2.5
Contributor: Riccardo Capelli
Submitted on: 09 Mar 2020
Last revised: 07 Sep 2020
Publication: R. Capelli, W. Lyu, V. Bolnykh, S. Meloni, J. M. H. Olsen, U. Rothlisberger, M. Parrinello, P. Carloni, Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study. The Journal of Physical Chemistry Letters. 11, 6373–6381 (2020)

PLUMED input files

File Compatible with
input_data/classical/FA-metaD/FA-MetaD_plumed.dat tested on v2.9 tested on master
input_data/classical/WT-metaD/WT-MetaD_plumed.dat tested on v2.9 tested on master
input_data/classical/ratchet/rMD_plumed.dat tested on v2.9 tested on master
input_data/classical/reweighting/reweighting.dat tested on v2.9 tested on master

Last tested: 18 Jun 2024, 14:28:24

Project description and instructions
This egg contains the structure and input files for the M2 muscarinic receptor with iperoxo calculations for both classical force field (with GROMACS 2018.6) and QM/MM (GROMACS+CPMD with MiMiC interface), the PLUMED files for Ratcheted MD (ratchet folder), well-tempered metadynamics (WT-MetaD folder), frequency-adaptive metadynamics (FA-MetaD), and reweighting procedure (reweighting).

Submission history
[v1] 09 Mar 2020: original submission
[v2] 23 May 2020: updated doi
[v3] 07 Sep 2020: updated doi

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