[gmx-users] inquiring for solving trjconv problems

Justin Lemkul jalemkul at vt.edu
Sun Jan 20 01:08:36 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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