[gmx-users] pbc whole

Carla Jamous carlajamous at gmail.com
Thu Feb 18 11:56:05 CET 2010

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?"
But anyhow, please can you send me the version of trjconv that does the


On Thu, Feb 18, 2010 at 11:42 AM, Tsjerk Wassenaar <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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