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 |   |
Last tested: 26 Jan 2024, 15:34:13
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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