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automated-lysozyme-water-forcefields-gromacs

Script developed to run the commands of the "Lysozyme in Water" tutorial in gromacs in different force fields at once

https://github.com/brendaferrari/automated-lysozyme-water-forcefields-gromacs

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
    Links to: acs.org
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  • ○
    Scientific vocabulary similarity
    Low similarity (6.5%) to scientific vocabulary

Keywords

automated gromacs lysozyme water
Last synced: 7 months ago · JSON representation ·

Repository

Script developed to run the commands of the "Lysozyme in Water" tutorial in gromacs in different force fields at once

Basic Info
  • Host: GitHub
  • Owner: brendaferrari
  • Language: Shell
  • Default Branch: master
  • Homepage:
  • Size: 34.2 KB
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
automated gromacs lysozyme water
Created almost 5 years ago · Last pushed about 3 years ago
Metadata Files
Readme Citation

README.md

Automated Lysozyme in Water tutorial in different force fields

Script developed to run the commands of the "Lysozyme in Water" tutorial in gromacs in different force fields at once. More information on how to execute this tutorial is found in Lysozyme in Water Tutorial

How to run the script

To run in this zipped file: Unpack this file, open the linux terminal and use the command

./script-dynamics.sh files/1aki.pdb files/

To run the script: open the linux terminal and use the command

./script-dynamics.sh input_path/file_name.pdb output_path/

Implemented force fields

  • Implemented on the root directory

(1) AMBER03 (5) AMBER99SB (6) AMBER99SB-ILDN (8) CHARMM27 (15) OPLS-AA/L

  • Implemented on the 'extraforcefields' directory (see more information in README.md at proper directory)

(9) GROMOS96 43a1 (10) GROMOS96 43a2 (11) GROMOS96 45a3 (12) GROMOS96 53a5 (13) GROMOS96 53a6 (14) GROMOS96 54a7

Water models used in this tutorial

  • spc to GROMOS96 43a1 and GROMOS96 53a6
  • tip3p to AMBER99SB, AMBER99SB-ILDN and CHARMM27
  • tip4p or spce to OPLS-AA/L

Observations

1. This script has been elaborated as a straight-forward way to execute all the commands in gromacs tutorial "Lysozyme in Water", but changes in parameters are necessary as the objective of the molecular dynamics changes.

2. All the parameters changes involving the script is presented above in this README. Other parameters may be found at Gromacs page or at the tutorial page presented in the begining of this description

3. I am not affiliated to Gromacs Team. I am a PhD Student trying to help others to have a quicker way to run this tutorial.

Authorship

Social preview original photo by Florian Olivo on Unsplash

Owner

  • Name: Brenda Ferrari
  • Login: brendaferrari
  • Kind: user

Chemistry PhD student - Python and Machine Learning student

Citation (CITATION.cff) 

cff-version: 0.0.1
message: "If you use this software, please cite it as below."
authors:
- family-names: "Ferrari"
  given-names: "Brenda"
  orcid: "https://orcid.org/0000-0001-5609-0947"
title: "automated-lysozyme-water-forcefields-GROMACS"
version: 0.0.1
doi: 10.5281/zenodo.7603643
date-released: 2023-02-03
url: "https://github.com/brendaferrari/automated-lysozyme-water-forcefields-GROMACS"

GitHub Events

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Last synced: about 2 years ago

All Time
  • Total Commits: 3
  • Total Committers: 2
  • Avg Commits per committer: 1.5
  • Development Distribution Score (DDS): 0.333
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  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
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brendaferrari b****i@g****m 2
Brenda Ferrari 6****i 1

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Last synced: about 2 years ago

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  • Average comments per issue: 0
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  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
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