[gmx-users] pbc whole

[Carla Jamous]

Hi Justin and Tsjerk,
Thank you for your answers, but I found a command that worked for me:)

First, I concatenated the ensemble of my trajectory.
& then, I did the following:

trjconv -s a.tpr -f traj.xtc -o traj1.xtc -pbc nojump -n b.ndx

Cheers,
Carla

On Thu, Feb 18, 2010 at 12:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Carla Jamous wrote:
>
>>
>> Hi Tsjerk,
>> sorry I didn't understand this part of your explanation:"Can you make an
>> image of the last frame and send a link
>> to it?"
>>
>
> Render an image of your system from the end of your trajectory and post it
> somewhere online (like photobucket); do not send it as an attachment to your
> email.
>
> -Justin
>
>  But anyhow, please can you send me the version of trjconv that does the
>> trick?
>>
>> Thanks,
>> Carla
>>
>> On Thu, Feb 18, 2010 at 11:42 AM, Tsjerk Wassenaar <tsjerkw at gmail.com<mailto:
>> tsjerkw at gmail.com>> wrote:
>>
>>    Hi Carla,
>>
>>     > I checked with genconf & now I'm certain that my ATP molecule is
>>    still with
>>     > the protein
>>
>>    That's good to know :)
>>
>>     >>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol
>>     >>> (centering on "Protein")
>>
>>    So what did come out of this then? It should have given you a compact
>>    representation of your system with the protein in the center. But if
>>    the protein's in the center and everything is put as close to that
>>    center as possible, which is what "compact" does, then the ATP should
>>    be there too. Can you make an image of the last frame and send a link
>>    to it? Alternatively, I have a patched version of trjconv that you can
>>    use to do the trick. I can send it if you want.
>>
>>    Cheers,
>>
>>    Tsjerk
>>
>>
>>    --
>>    Tsjerk A. Wassenaar, Ph.D.
>>
>>    Computational Chemist
>>    Medicinal Chemist
>>    Neuropharmacologist
>>    --
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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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