Project ID: plumID:19.022
Name: eABF simulation of NANMA (alanine dipeptide)
Archive: https://github.com/HanatoK/eABF_plumed_examples/raw/master/eABF_NANMA_gmx.zip
Category: methods
Keywords: eABF, DRR, alanine dipeptide
PLUMED version: 2.4
Contributor: Haochuan Chen
Submitted on: 30 Apr 2019
Publication: H. Chen, H. Fu, X. Shao, C. Chipot, W. Cai, ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines, Journal of Chemical Information and Modeling 58, 1315–1318 (2018)

PLUMED input files

File Compatible with
plumed.dat tested on v2.6 tested on master

Last tested: 09 Dec 2019, 15:35:17

Project description and instructions
The software used is GROMACS version >2018.6. Assuming GROMACS is installed as /usr/local/gromacs/bin/gmx and compiled with PLUMED support, you can run: /usr/local/gromacs/bin/gmx mdrun -ntomp 8 -s ./alad_600ns.tpr -plumed ./plumed.dat& After the simulation, you can extract the gradients from the .drrstate file using plumed drr_tool --extract ./alad.drrstate -v and then integrate the alad.czar.grad file by abf_integrate alad.czar.grad The abf_integrate program can be found at here

Submission history
[v1] 30 Apr 2019: original submission

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plumeDnest:19.022