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

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 9 22:36:36 CET 2010

ms wrote:
> Hi,
> I am doing REMD simulations of multiple homopolymeric peptides in a PBC 
> box, in vacuum (it's a custom coarse grain). GROMACS 4.0.5. I want to 
> analyze features of the system that require to use g_gyrate to find out 
> the moments of inertia of the system, for example.
> I understand g_gyrate is one of the few tools that is *not* PBC aware. I 
> am trying therefore to correct my REMD trajectories using several 
> variants of trjconv, with simple command lines like:
> trjconv -f xac_12855257520.xtc -o xac_12855257520_pbcatom.xtc -pbc nojump
> ...but alas, when I see them with ngmx, the peptides tend to break. I 
> tried both pbc nojump and pbc atom, with same results (pbc nojump 
> perhaps is a bit worse). I can't use pbc cluster because they're not 
> always clustered and I am interested in both the clustered and 
> non-clustered states.
> I'd like to give more information about that but I don't really know 
> what is relevant to debug this kind of issue. I looked in the mailing 
> list but (despite multiple woes about pbc nojump etc.) I didn't find a 
> helpful thread. Any hint?

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.


> thanks!
> Massimo


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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