My Gromacs Tutorial

Examples of commands for running gromacs jobs grompp Prepare a topol.tpr file for a serial job and then for 4-CPU-parallel one linux01>grompp -f md.mdp -po mdout.mdp -c md.gro -r md_out.gro -n md.ndx -p md.top -o topol.tpr linux02>grompp -f md.mdp -po mdout.mdp -c md.gro -r md_out.gro -n md.ndx -p md.top -o topol.tpr -np 4 & mdrun Run a serial job and then 4-CPU-parallel with MPICH1 or LAM linux01>mdrun -f topol.tpr -o md.trr -x md.xtc -c md_out.gro -e md.edr -g md.log & linux02>mpirun -np 4 /usr/local/share/gromacs331/bin/mdrun -f topol.tpr -o md.trr -x md.xtc -c md_out.gro -e md.edr -g md.log -np 4 & or linux02>mpirun -np 4 /usr/local/share/gromacs331/bin/mdrun -f topol.tpr -o md.trr -x md.xtc -c md_out.gro -e md.edr -g md.log & mdrun Run a serial job of umbrella sampling MD simulations linux01>grompp -f md.mdp -po mdout.mdp -c md.gro -r md_out.gro -n md.ndx -p md.top -o topol.tpr linux02>mdrun -f topol.tpr -o md.trr -x md.xtc -c md_out.gro -e md.edr -g md.log -pi umbrella.ppa -pn umbrella.ndx -po umbrella_out.ppa -pd umbrella.pdo & mdrun Run a serial job of steered MD simulations linux01>grompp -f md.mdp -po mdout.mdp -c md.gro -r md_out.gro -n md.ndx -p md.top -o topol.tpr linux02>mdrun -f topol.tpr -o md.trr -x md.xtc -c md_out.gro -e md.edr -g md.log -pi pull.ppa -pn pull.ndx -po pull_out.ppa -pd pull.pdo &