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

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Nov 5 23:10:48 CET 2010


Do the holes match the parts of the protein sticking out on the other side?


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

> where exactly is yours? i am simulating with that solvent at the moment
> 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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