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Publication: unpublished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 tested on v2.6 tested on master
plumed.1.dat tested on v2.6 tested on master
plumed_be-common.dat tested on v2.6 tested on master

Last tested: 15 Oct 2019, 20:02:19

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

Badge
Click on the image below and get the code to add the badge to your website!
plumeDnest:19.059