Hello,<div><br></div><div>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. </div><div><br></div>
<div><br></div><div>Diana <br><br><div class="gmail_quote">On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<p>Hey,</p>
<p>Do the holes match the parts of the protein sticking out on the other side? </p>
<p>Tsjerk</p>
<p></p><blockquote type="cite"><div>On Nov 5, 2010 8:14 PM, "Vitaly Chaban" <<a href="mailto:vvchaban@gmail.com" target="_blank">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" target="_blank">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>
</div><p><font color="#500050">>>
>> Diana -
>>
>> I just wonder how the density of your system behaves while you run NPT
>> equili...</font></p></blockquote><p></p>
<br>--<br>
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Protein Modeling Laboratory<br>ITQB/UNL<br>Oeiras, Portugal<br>
</div>