Removing pbc effect

Your commands are possibly not working because they centre the protein based on the centre of mass, which is the same point if the chains are together or wrapped over the periodic boundary conditions.

What you should try is making an index group using ‘gmx make_ndx’ that contains the atom numbers of one of the protein chains. Let’s say you name the index file “chain_index.ndx”.

Then try the following command (using your original trajectory as the input):

gmx trjconv -s md.tpr -f md.trr -n chain_index.ndx -pbc mol -ur compact -center -o md1.trr

Choose the group you made containing the atoms of one of the chains for centering and then “System” for output. Hopefully that works!

1 Like