[gmx-users] inquiring for solving trjconv problems

[Justin Lemkul]

On 1/19/13 5:21 PM, Mehdi Bagherpour wrote:
> hello everybody
>
> I have simulated DNA using CHARMM force field for 50 ns with 2 ps snapshots
> for each step.
> when I wanted to convert .xtc trajectory files to .pdb using trjconv,  some
> of the snapshots were collaborated.
> I have used periodic boundary conditions in this simulations.
> To convert, I used bellow command:
>
> trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center
>
> In collaborated .pdb files two strands of DNA separated from each other.
> when I used bellow command instead of above command, this collaborated .pdb
> file will be corrected,
> but some of the other .pdb files will be ruined as same as
>
> trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol
>
> would you please help me to solve this technical problem?
>

Use -center, perhaps in conjunction with some custom index group that will serve 
as an adequate central group for processing.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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