[gmx-users] inquiring for solving trjconv problems

[Mehdi Bagherpour]

I use bellow commands but still in some of snapshot trajectories, two
strand of DNA separated from each other in VMD.


trjconv -s md.tpr -f md.xtc -o md.pdb  -center

trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -ur compact

trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center -ur compact

trjconv -s md.tpr -f md.xtc -o md.pdb -center -ur compact


On Sun, Jan 20, 2013 at 3:38 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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