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Publication: unpublished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: 22 Apr 2025, 10:14:54
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.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 19 Jul 2019: original submission
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