On 09/11/10 21:36, Justin A. Lemkul wrote:
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.
Excellent advice; it seems to do exactly what I want. Thanks a lot!!
Massimo
-Justin
thanks!
Massimo
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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