A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.
Python 20.93%Shell 53.62%Perl 25.44%
gromacs-scripts's Introduction
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...
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Simple MD
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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
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Path Sampling
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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
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Analysis
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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