[gmx-users] Re: genbox generating acetonitrile box with holes

[Diana Lousa]

Hello,

No, the hole don't correspond to parts of the protein sticking out on the
other side. The protein is in the center of the box and the holes are not
due to pbc issues.


Diana

On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hey,
>
> Do the holes match the parts of the protein sticking out on the other side?
>
>
> Tsjerk
>
> On Nov 5, 2010 8:14 PM, "Vitaly Chaban" <vvchaban at gmail.com> wrote:
>
> On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz <vedat.durmaz at gmx.net> wrote:
> > hi vitaly,
> >
> > the only acetonitrile boxe that i was able to find is the one provided by
> > christoph freudenberger in 2003:
> >
> > http://www.gromacs.org/@api/deki/files/34/=mecn_box.tgz
>
> Maybe somewhere on other old website if they lost it while migrating
> to the new one - there should have been a few carbon nanotubes + ACN
> systems. If you need a 6-point ACN box, I can find it on my own
> archives.
>
> > where exactly is yours? i am simulating with that solvent at the moment
> but
> > the charges are different from the the ones mentioned above .. and the
> > density is a little less than it should be (640g/ml).
>
> Hmm... Is 640 kg/m3 the density with protein? What it should be then
> (if with protein)?
>
> The density of the bulk ACN is 770kg/m3 at 300K, and the model, which
> we used, reproduces it perfectly.
>
> -
> Dr. Vitaly V. Chaban
>
>
>
> > Am 05.11.2010 19:16, schrieb Vitaly Chaban:
>
> >> >> Diana - >> >> I just wonder how the density of your system behaves
> while you run NPT >> equili...
>
>
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-- 
Diana Lousa
PhD student
Protein Modeling Laboratory
ITQB/UNL
Oeiras, Portugal
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