Project ID: plumID:24.008
Name: yCD Metadynamics
Archive: https://github.com/mccartygroup/yCD_Metadynamics/raw/main/yCD_Metadynamics.zip
Category: bio
Keywords: volume-based MetaD, path CVs, infrequent MetaD, product release
PLUMED version: 2.4
Contributor: James McCarty
Submitted on: 19 Mar 2024
Publication: K. A. Croney, J. McCarty, Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics. The Journal of Physical Chemistry B. 128, 3102–3112 (2024)

PLUMED input files

File Compatible with
5FU/Volume_MetaD_Input/plumed_run.dat tested on v2.10 tested on master
5FU/iMetaD_Input/plumed_imetad.dat tested on v2.10 tested on master
Reweighting/plumed_get_weights.dat tested on v2.10 tested on master
Reweighting/plumed_reweight.dat tested on v2.10 tested on master
Uracil/Volume_MetaD_Input/plumed_run.dat tested on v2.10 tested on master
Uracil/iMetaD/plumed_imetad.dat tested on v2.10 tested on master

Last tested: 22 Apr 2025, 10:00:14

Project description and instructions
All input files to simulate yCD with 5-FU bound or uracil bound are provided in the Structure folder. In the Volume_MetaD_Input is the plumed input for running volume based metadynamics. All the necessary files are in the Structure folder. In the iMetaD folder is the plumed input for running unbinding simulations used to estimate k_off from infrequent metadynamics. Plumed inputs for post-processing and reweighting are in the Reweighting directory.

Click here to open manual pages for actions used in this project.

Submission history
[v1] 19 Mar 2024: original submission

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