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.
-Justin
thanks!
Massimo
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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