[gmx-users] inquiring for solving trjconv problems

[Justin Lemkul]

On 1/20/13 7:34 AM, Mehdi Bagherpour wrote:
> 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
>

None of these involve an index group.  As I said, you may have to choose some 
custom subset of atoms to serve as a centering group.  The -center option places 
the geometric center of the chosen group at the center of the box; if there are 
two molecules, then the center of this group can still coincide with the center 
of the unit cell if both molecules are at opposite sides of the box.

-Justin

>
> 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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-- 
========================================

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

========================================