[gmx-users] pbc whole

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 15 16:32:49 CET 2010

Carla Jamous wrote:
> 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?

You may need several more iterations of trjconv (one rarely does the trick), 
employing -pbc nojump, -pbc cluster, and/or -center.  For protein-ligand 
complexes, I have often found that the combination of:

trjconv -pbc mol -ur compact -center

(centering on "Protein")

does the trick.  And it makes molecules whole, as well :)  I think there are 
also some breakdowns (documented somewhere in the list archive) when applying 
-fit and -pbc in the same step.  I believe it is recommended to fix PBC first, 
then applying any sort of fitting in a separate, subsequent step.


> Thank you
> Carla


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list