https://github.com/kull-centre/_2023_kummerer_nmrff
Science Score: 31.0%
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Found 3 DOI reference(s) in README -
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Low similarity (6.9%) to scientific vocabulary
Last synced: 4 months ago
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Basic Info
- Host: GitHub
- Owner: KULL-Centre
- Language: Jupyter Notebook
- Default Branch: main
- Size: 571 MB
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Created about 3 years ago
· Last pushed about 3 years ago
https://github.com/KULL-Centre/_2023_Kummerer_nmrFF/blob/main/
# Data, scripts and notebooks to analyse the simulations from: ref Content: - ```setup_md/``` contains mdp files, force field files, examplary setup scripts and everything else need to set up the MD simulations for each system. - ```specdens_mapping/``` contains example scripts to calculate NMR relaxation rates using the spectral density mapping approach (https://pubs.acs.org/doi/10.1021/acs.jctc.0c01338, https://doi.org/10.1039/C8CP03915A). - ```reweighting/``` contains scripts to perform k-fold cross validation to determine an adequate $\theta$ for reweighting with ABSURDer. - ```notebooks/``` contains Jupyter notebooks to recreate all the plots in the main and SI of the manuscript and a current version of ABSURDer. - ```data/``` contains all the data relevant to recreate the plots. - ```modify_topology/``` contains a pyhton script that can be used to modify a GROMACS topology file implementing our force field changes. Only tested on the AMBER force field a99SB*-ILDN. Usage: ```python moddihed_ffAMBER.py topology.top``` Trajectories and other simulation files are available at:
Download link will be available soon.
Owner
- Name: Linderstrøm-Lang Centre for Protein Science, University of Copenhagen
- Login: KULL-Centre
- Kind: organization
- Location: Copenhagen, Denmark
- Website: https://www1.bio.ku.dk/english/research/bms/research/llc/
- Repositories: 8
- Profile: https://github.com/KULL-Centre