GitHub - NKM-ML/gromacs-scripts: A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.

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A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.

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Name		Name	Last commit message	Last commit date
Latest commit History 87 Commits
analysis		analysis
automate		automate
cluster		cluster
mdp		mdp
pdb		pdb
perl		perl
topologies		topologies
README		README

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gromacs-scripts are a collection of scripts to be used in conjunction with gromacs for a wide range of things: data processing, trajectory generation, input files, topologies...

============================
	Simple MD
============================
cluster/cluster_equilibrate.sh:
>> mdp/fmo/em_directions.mdp
>> mdp/fmo/nvt_directions.mdp
>> mdp/fmo/npt_directions.mdp
>> mdp/smy_neq/em.mdp
>> mdp/smy_neq/e_nvt.mdp
>> mdp/smy_neq/e_npt.mdp

cluster/cluster_mdrun.sh:
>> mdp/fmo/CtExcite.4.6.mdp
>> mdp/fmo/md_directions.mdp
>> mdp/smy_neq/CtExcite.mdp
>> mdp/smy_neq/CtGround.mdp

=============================
	Path Sampling
=============================
cluster/cluster_traj_prepare.sh: 
>> mdp/fmo/traj_spacer.mdp

cluster/cluster_traj_submit.sh:
>> mdp/fmo/traj_micro_spacer.mdp
>> mdp/fmo/Traj.4.6.mdp

=============================
	Analysis
=============================
analysis/average_traj.py: Takes a collection of .xvg files as an argument and returns the average of the energies as a function of time.
analysis/autocorrelate.py: Takes a long .xvg file and spits out the correlation function