[gmx-users] genconf -trj?!?

[Justin A. Lemkul]

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

-- 
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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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