Essential gromacs commands!

Hey ,

Many of you might want to use gromacs or are using it now. Gromacs is used the most by the bio-community to perform molecular dynamic simulations on bio molecules. I have compiled a list of commands which would help you from the start to the end.

1) pdb2gmx -f pdbid.pdb -o pdbid_processed.gro -water spce

2) editconf -f pdbid_processed.gro -o pdbid_box.gro -c -d 1.0 -bt cubic

3) genbox -cp pdbid_box.gro -cs spc216.gro -o pdbid_solvated.gro -p topol.top

4) grompp -f minimization.mdp -c pdbid_solvated.gro -p topol.top -o minpdbid.tpr

5) mdrun -v -deffnm minpdbid

6) grompp -f nvt.mdp -c minpdbid.gro -p topol.top -o nvtpdbid.tpr

7) mdrun -v -deffnm nvtpdbid

8) grompp -f npt.mdp -c nvtpdbid.gro -t nvtpdbid.trr -p topol.top -o nptpdbid.tpr

9) mdrun -v -deffnm nptpdbid

10) grompp -f mdrun.mdp -c nptpdbid.gro -t nptpdbid.trr -e nptpdbid.edr -p topol.top -o mdpdbid.tpr

11) mdrun -v -deffnm mdpdbid

Note that all .mdp files contain all the configurations. You can have your own file saved in the folder. I have not attached those files.