[gmx-users] pbc whole

Carla Jamous carlajamous at gmail.com
Tue Feb 16 16:07:45 CET 2010

Hi Justin,
Thank you for your answer but I'm still not getting my ligand to stay in the

I tried the following(after taking a look at the mailing list archive):

trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol (centering
on "Protein")
trjconv -s d.tpr -f c.xtc -o f.xtc -fit rot+trans

So please do you have another advise to give me?


On Mon, Feb 15, 2010 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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.
> -Justin
>  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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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