[gmx-users] trjconv, pbc and breaking of multiple peptides

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 10 22:34:27 CET 2010

ms wrote:
> On 09/11/10 21:36, Justin A. Lemkul wrote:
>> There are numerous -pbc options with trjconv; have you tried others? I
>> have never had luck with -pbc nojump actually working, and -pbc atom
>> provides no guarantee that molecules will be properly reconstructed.
>> Using -pbc mol -center is often a much better approach, in my experience.
> I spoke too soon. -pbc mol -center doesn't indeed break molecules, but 
> it doesn't seem to always work correctly -I evidently continue to have 
> frames where the system is obviously not centered correctly in the box, 
> so even if I have a compact conglomerate of my molecules, the calculated 
> gyration radius is artificially large (In fact, I discovered the issue 
> by looking at the frames with large gyration radiuses).
> I am sure it doesn't work correctly because if I visualize the system in 
> VMD, enabling periodic copies I see the correct (compact) structure at 
> the corners between boxes. - I can provide pictures if needed.
> Any idea on how to proceed? I am quite lost. I wouldn't like to rewrite 
> g_gyrate by myself :)

I presume you're centering on "Protein" in this case?  You can create a custom 
index group (perhaps towards the center of one of your peptides) and center 
about it.  The -center function will locate the center of mass of the chosen 
group at the center of the box, so, in a simple case (i.e. a dimer) you would 
have two peptides at the corners, but the center of mass still located at the 
box center.  Choosing one residue of one of the monomers has, in my experience, 
solved this issue when centering about Protein has not worked.


> thanks!
> m.


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


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