My Gromacs Tutorial

Examples of commands for analysing results trjconv Prepare a restart file (-b and -e options are in ps) trjconv -f traj.trr -o restart.gro -s topol.tpr -n index.ndx -b 871 -e 871 trjcat Merge all restart trajectory files (*.xtc or *.trr) to a file traj_full.xtc. trjcat -o traj_full.xtc -f *.xtc -settime g_traj Filter only z-coordinates g_traj -f traj.xtc -s topol.tpr -n md.ndx -ox z_coordinate.xvg -nox -noy g_rms Calculate RMSD g_rms -s md_start.gro -f traj.xtc -n md.ndx -o rmsd.xvg g_wham Calculate WHAM histogram and free energy for umbrella sampling MD simulations Firstly, calculate min and max values for 700 ps (from 200 ps to 1000 ps) for 5 MD trajectories, then, calculate histogram and free energy with tolerance 1e-5 and number of bins 100: linux01> /gromacs-3.2.1-LBM/bin/g_wham -noprof -temp 300 -b 200 -e 1000 -tu ps set01.pdo.gz set02.pdo.gz set03.pdo.gz set04.pdo.gz set05.pdo.gz & linux02> /gromacs-3.2.1-LBM/bin/g_wham -temp 300 -b 200 -e 1000 -tu ps -min 0.5290 -max 0.6449 -tol 1e-5 -bins 100 set01.pdo.gz set02.pdo.gz set03.pdo.gz set04.pdo.gz set05.pdo.gz &