My Gromacs Tutorial

Examples of commands for building coordinates and topologies pdb2gmx Prepare topology *.top input file from *.pdb format pdb2gmx -f md.pdb -o md.gro -p md.top -ter -glu -his editconf Convert *.gro to *.pdb format and vice versa linux01>editconf -f md.gro -o md.pdb linux02>editconf -f md.pdb -o md.gro make_ndx Prepare index file linux01>make_ndx -f md.gro -o md.ndx linux02>make_ndx -f md.gro -n md.ndx -o new_index.ndx make_ndx Interactive commands and an example | or & and &! and not (all except for) ! not 15&!22 all atoms of the group 15 except for atoms of the group 22