Project ID: plumID:25.013
Name: Data-Driven Engineering of Highly Thermostable Collagen-Mimetic Peptoid Triple Helices
Archive: https://github.com/alexberlaga/cmp_plumed_nest/archive/refs/heads/main.zip
Category: bio
Keywords: umbrella sampling, temperature ramping
PLUMED version: 2.9
Contributor: Alexander Berlaga
Submitted on: 19 May 2025
Publication: unpublished
PLUMED input files
| File | Compatible with |
|---|---|
| annealing/plumed0.dat |   |
| umbrella/plumed.dat | |
Last tested: 29 May 2025, 06:50:06
Project description and instructions
This repository has the necessary code to run annealing and umbrella simulations of collagen-mimetic peptoids. Files are organized as follows. The Annealing Folder contains initial structure (npt.gro) and topology files (topol.top); Code generating PLUMED files to track CVs (gen_plumed.py); molecular dynamics parameters for annealing (npt_run.mdp); Example PLUMED file (plumed0.dat); code to run the MD (anneal.sbatch and run_sim.py). The Umbrella Folder contains initial structure (npt.gro) and topology files (topol.top); Code generating TICA object and PLUMED files to bias CVs (make_tica_plumed.py); molecular dynamics parameters for equilibration and umbrella runs (umbrella_equil.mdp and umbrella_run.mdp, respectively); Example PLUMED file (plumed.dat); code to run the MD (run_umbrella.sbatch).
Click here to open manual pages for actions used in this project.
Submission history
[v1] 19 May 2025: original submission
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