[gmx-users] pbc whole

Carla Jamous carlajamous at gmail.com
Mon Feb 15 16:26:59 CET 2010

Hi everyone,
I'm using this command to extract my protein and my ligand from the

trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n
prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj

Before, I had a problem with residues of my protein showing at the other end
of the box, when I display my .xtc with VMD.
the "-pbc whole" fixed it.

However, now I have another issue: my ligand is at the other end of the box.
So please can anyone tell me what can I do to fix that and get a reasonable
RMSD value?

Thank you
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