I am concerned about the number density of water. At T = 300 K and P = 1 atm, SPC/E water has certain number density (no. of molecules/nm^3). With genbox I get .gro file with 34.04 molecules/nm^3 number density, which will remain constant even if I do equilibration in NVT simulation set up. So does that 34.04 molecules/nm^3 corresponds to thermodynamic condition of water at 300K and 1 atm. <br>
<br>thanks<br>sikandar<br><br><div class="gmail_quote">On Fri, Jun 18, 2010 at 12:20 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5">On 2010-06-18 18.24, Sikandar Mashayak wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi<br>
<br>
When a bulk SPC/E water box(.gro) is created using the command "genbox<br>
-cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic condition of<br>
water?<br>
<br>
Is it 300K at 1atm?<br>
<br>
thanks<br>
sikandar<br>
<br>
</blockquote></div></div>
No. You have to equilibrate because the box is not completely full.<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br><font color="#888888">
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