<p>Hey,</p>
<p>Do the holes match the parts of the protein sticking out on the other side? </p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Nov 5, 2010 8:14 PM, "Vitaly Chaban" <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>> wrote:<br><br>On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz <<a href="mailto:vedat.durmaz@gmx.net">vedat.durmaz@gmx.net</a>> wrote:<br>
> hi vitaly,<br>
><br>
> the only acetonitrile boxe that i was able to find is the one provided by<br>
> christoph freudenberger in 2003:<br>
><br>
> <a href="http://www.gromacs.org/@api/deki/files/34/=mecn_box.tgz" target="_blank">http://www.gromacs.org/@api/deki/files/34/=mecn_box.tgz</a><br>
<br>
Maybe somewhere on other old website if they lost it while migrating<br>
to the new one - there should have been a few carbon nanotubes + ACN<br>
systems. If you need a 6-point ACN box, I can find it on my own<br>
archives.<br>
<br>
> where exactly is yours? i am simulating with that solvent at the moment but<br>
> the charges are different from the the ones mentioned above .. and the<br>
> density is a little less than it should be (640g/ml).<br>
<br>
Hmm... Is 640 kg/m3 the density with protein? What it should be then<br>
(if with protein)?<br>
<br>
The density of the bulk ACN is 770kg/m3 at 300K, and the model, which<br>
we used, reproduces it perfectly.<br>
<br>
-<br>
Dr. Vitaly V. Chaban<br>
<br>
<br>
<br>
> Am 05.11.2010 19:16, schrieb Vitaly Chaban:<br>
<p><font color="#500050">>>
>> Diana -
>>
>> I just wonder how the density of your system behaves while you run NPT
>> equili...</font></p></blockquote></p>