Project ID: plumID:26.014
Name: Dissociation free energy (DFE) calculationsfor GPR15L–polySia
Archive: https://github.com/gcourtade/papers/raw/master/2026/GPR15L_polySia/plumed_nest.zip
Category: bio
Keywords: metadynamics, protein-carbohydrate interaction
PLUMED version: 2.8.3
Contributor: Davide Luciano and Gaston Courtade
Submitted on: 01 Sep 2026
Publication: unpublished
PLUMED input files
| File | Compatible with |
|---|---|
| DP10/plumed.dat |   |
| DP20/plumed.dat | |
| DP5/plumed.dat | |
Last tested: 01 Sep 2026, 14:14:08
Project description and instructions
1) build solvated, neutralized system (see unbiased_run.sh header) with editconf -> solvate -> genion -> emin.mdp. 2) one long unbiased reference trajectory with ./unbiased_run.sh (slurm job; grompp mdp/{nvt,npt,md}.mdp then mdrun). 3) metadynamics replica ensemble with ./run.sh (regenerates plumed.dat, loops rep_i with seeded velocities; grompp nvt_seeded.mdp -> npt.mdp -> md_short.mdp + plumed). run.sh writes plumed.dat itself and is self-contained apart from cluster environment variables ($gmx, $plumed, PLUMED_KERNEL) — adjust the paths at the top for your installation. Seeds are derived from BASE_SEED to make the ensemble reproducible.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 01 Sep 2026:
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