On 5/9/12 11:59 AM, Faezeh Kargar wrote:
Dear all,
my coarse grained simulations contain a cubic box with 16 peptides. After 85ns
peptides aggregate but because of PBC I have problem in analyzing some data like
radius of gyration and clustering. I searched mailing list to solve this problem
by trjconv. I examined its different options but without any results. casually
genconf came in my mind. I want to use this command for a trajectory with option
-trj
genconf -f .tpr -trj .xtc/.gro -o .gro -nbox 2 1 1
but when I use it I face with "Segmentation fault". I searched mailing list and
found just one
question"http://lists.gromacs.org/pipermail/gmx-users/2004-July/011196.html";
whithout answer.
It's almost certainly a bug, but the fact that no one has asked about the -trj
option in nearly eight years suggests it's probably not a high priority to fix,
or simply that no one ever noticed it. In any case, genconf is not likely to be
a suitable solution.
Please guide me wheather this command can help me to generate an aggregated
system for analyzing? If Yes, How? If No help me please?
You need trjconv, and likely several instances of it. Complex systems like
these require great care and potentially custom index groups. There is a
generic trjconv workflow here:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
There are also numerous posts in the list archive regarding clustering of
various molecules, including peptides and micelles. The tips there will likely
guide you, but if you need further help you'll need to provide explicit commands
that you've tried, what they produced, and why it's not what you're after. The
solution is in trjconv, but without knowing what you've tried, it's hard to
provide additional help.
-Justin
--
========================================
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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