[gmx-users] pbc whole

[Justin A. Lemkul]

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

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