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

ms devicerandom at gmail.com
Wed Nov 10 22:21:00 CET 2010

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 :)


Massimo Sandal, Ph.D.

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