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
jiaozihao18/gromacs-scripts
A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.
Shell