Project ID: plumID:19.059
Name: cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide
Archive: https://github.com/fabsugar/plumed-nest-files/raw/master/AAPAK_input.zip
Category: bio
Keywords: bias-exchange metadynamics, cis-trans isomerization
PLUMED version: 2.2.3
Contributor: Fabrizio Marinelli
Submitted on: 19 Jul 2019
Publication: unpublished
PLUMED input files
| File | Compatible with |
|---|---|
| plumed.0.dat |   |
| plumed.1.dat | |
| plumed_be-common.dat | |
Last tested: 23 Apr 2025, 10:28:07
Project description and instructions
The deposited files contain the necessary input to run bias-exchange metadynamics simulations to investigate the cis-trans isomerization of the Ac-Ala-Ala-Pro-Ala-Lys-NH2 peptide using two replicas, each one using a specific torsion angle as collective variable. The simulations were performed using GROMACS VERSION 5.0.2 and PLUMED VERSION 2.2.3. The simulations can be run for example using the command “mpirun -np 4 gmx_mpi mdrun -deffnm metad-be -plumed plumed -multi 2 -replex 2000 > & meta-be.out &”. Newer versions of GROMACS are able to read the .tpr files and run the simulations as well as newer versions of PLUMED.
Submission history
[v1] 19 Jul 2019: original submission
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