http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html Visualize ========= $ vglrun /opt/apps/VMD/vmd-1.9.2-install/bin/vmd 1AKI.pdb gmx_mpi pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) gmx_mpi editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic gmx_mpi solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top gmx_mpi grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr gmx_mpi genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8 Group 13 ( SOL) has 36846 elements gmx_mpi grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr gmx_mpi mdrun -v -deffnm em -nb gpu gmx_mpi energy -f em.edr -o potential.xvg At the prompt, type "10 0" to select Potential (10); zero (0) terminates input. gnuplot potential.plt gmx_mpi grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr gmx_mpi mdrun -v -deffnm nvt -nb gpu gmx_mpi energy -f nvt.edr -o energy.xvg Type "15 0" at the prompt to select the temperature of the system and exit. gnuplot energy.plt gmx_mpi grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr gmx_mpi mdrun -v -deffnm npt -nb gpu gmx_mpi energy -f npt.edr -o pressure.xvg Type "16 0" at the prompt to select the pressure of the system and exit. gmx_mpi energy -f npt.edr -o density.xvg gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr gmx_mpi mdrun -deffnm md_0_1 -nb gpu vglrun /opt/apps/VMD/vmd-1.9.2-install/bin/vmd md_0_1.gro (also load trajectory file: md_0_1.trr) extensions -> vis -> movie maker gmx_mpi trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact Select 0 ("System") for output. gmx_mpi rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns Choose 4 ("Backbone") for both the least squares fit and the group for RMSD calculation. gmx_mpi rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns gmx_mpi gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg