[gmx-users] pbc whole

[Carla Jamous]

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

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
Carla
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100215/898c04e6/attachment.html>