Project ID: plumID:20.026
Name: Free energy calculations of the functional selectivity of 5-HT_2B-TS G protein-coupled receptor
Archive: https://zenodo.org/record/4085006/files/plumed-nest.zip
Category: bio
Keywords: Metadynamics, Umbrella sampling
PLUMED version: 2.5
Contributor: Brandon Peters
Submitted on: 05 Oct 2020
Last revised: 15 Jan 2021
Publication: B. L. Peters, J. Deng, A. L. Ferguson, Free energy calculations of the functional selectivity of 5-HT2B G protein-coupled receptor. PLOS ONE. 15, e0243313 (2020)
PLUMED input files
| File | Compatible with |
|---|---|
| plumed.dat |   |
| plumed_WTMD.dat | |
Last tested: 17 Apr 2024, 07:24:27
Project description and instructions
There are the input files for well tempered metadynamics (WTMD) and umbrella sampling for 5-HT2B GPCR simulations with ligand, LSD. I run the PLUMED script as given for WTMD, “gmx grompp -f md.mdp -c lsd_final.gro -p topol.top -n index.ndx -o md_0_1_plumed.tpr” and “mpiexec mdrun_mpi -ntomp 2 -deffnm md_0_1_plumed -plumed plumed_WTMD.dat” and finally “plumed sum_hills –hills hills –outfile fes-lsd-final.dat”. Then I run “python 2Dplot_contour_plumed” which gives the Free Energy Surface and the history of hills. I ran the script for restraint. “gmx grompp -f md.mdp -c lsd-final.gro -p topol.top -n index.ndx -o md_final_plumed_startnew2.tpr” and “gmx mdrun -ntmpi 1 -ntomp 16 -v -deffnm md_final_plumed_startnew2 -plumed plumed_restrain.dat”. I follow this tutorial closely using “create-restraint.sh”.
Submission history
[v1] 05 Oct 2020: original submission
[v2] 15 Jan 2021: updated doi
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