https://github.com/brendaferrari/lysozyme-water-gromacs-script
Script developed to run the commands of the "Lysozyme in Water" tutorial in gromacs.
https://github.com/brendaferrari/lysozyme-water-gromacs-script
Science Score: 10.0%
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○Scientific vocabulary similarity
Low similarity (5.1%) to scientific vocabulary
Keywords
Repository
Script developed to run the commands of the "Lysozyme in Water" tutorial in gromacs.
Basic Info
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- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
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Topics
Metadata Files
README.md
Lysozyme in Water script
Script developed to run the commands of the "Lysozyme in Water" tutorial in gromacs, 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
./dynamics.sh files/1aki.pdb files/
To run the script: open the linux terminal and use the command
./dynamics.sh input_path/file_name.pdb output_path/
Force field parameters
(1) AMBER03 (5) AMBER99SB (6) AMBER99SB-ILDN (8) CHARMM27 (9) GROMOS96 43a1 (10) GROMOS96 43a2 (11) GROMOS96 45a3 (12) GROMOS96 53a5 (13) GROMOS96 53a6 (14) GROMOS96 54a7 (15) OPLS-AA/L
Water model
- 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
- Author: Brenda Ferrari brendaferrari
- Review: Lucas Andrade lbertoncello
Owner
- Name: Brenda Ferrari
- Login: brendaferrari
- Kind: user
- Repositories: 6
- Profile: https://github.com/brendaferrari
Chemistry PhD student - Python and Machine Learning student
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| Name | Commits | |
|---|---|---|
| brendaferrari | b****i@g****m | 3 |
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