Hi Justin<br><br>Thank you for your suggestion.<br><br>Regards<br>Vinoth<br><br><div class="gmail_quote">On Mon, Sep 27, 2010 at 4:52 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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 class="im"><br>
<br>
vinothkumar mohanakrishnan 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 justin<br>
<br>
if genbox is not able to find sufficient space then why should one calculate number density for the given box dimension?.similarly the the <br>
</blockquote>
<br></div>
Just because you can calculate a certain number density does not necessarily mean that the algorithm genbox is using can produce such a configuration. It inserts molecules randomly, so you may be able to find a magical value of -seed for which this will work. The simpler approach is what I suggested earlier.<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
number of molecules are not getting updated in the molecules section of the topology file when inserting multiple molecules using the genbox command. everytime i need to update it <a href="http://manually.is" target="_blank">manually.is</a> <<a href="http://manually.is" target="_blank">http://manually.is</a>> there a way to update it automatically?<br>
<br>
</blockquote>
<br>
The topology will only be updated automatically when adding water. Otherwise, you have to do it yourself.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Regards<br>
Vinoth<div class="im"><br>
<br>
On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
vinothkumar mohanakrishnan wrote:<br>
<br>
Hi all<br>
<br>
I have a diffculty in adding multiple molecules of hexane to my<br>
box. my box size is 4.72*2.36*2.36 (nm) according to my number<br>
density calculations the box should fit 124 molecules of hexane<br>
whereas it adds only 76 molecules to the box below is my<br>
command. i had evev tried with -try command but without sucess.<br>
<br>
genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o<br>
hexane-multi.gro -nmol 124 -seed 1268<br>
<br>
<br>
If you're not getting all the molecules you want, then genbox is<br>
unable to find sufficient space for them. Try a larger box, then<br>
equilibrate.<br>
<br>
-Justin<br>
<br>
Regards<br>
Vinoth<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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