README

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