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On 1/05/2012 12:20 PM, cuong nguyen wrote:
<blockquote
cite="mid:CAMj9MaeLpTeB2gyMn_ZGA41HxgoZcJD+WX6S2crZq=5OnC7jmg@mail.gmail.com"
type="cite">Thanks,<br>
<br>
I tried to add -maxsol 846 to the command and got the box with 846
water molecules. However, when I use VMD to visualize the box,
these molecules concentrate on 1/3 the box space. I do need the
molecules to spread out whole box.<br>
<br>
</blockquote>
<br>
So next time think about asking the question whose answer you
actually want... Do some arithmetic and put a suitable box around a
single water molecule. Then replicate with genconf, like I suggested
last time.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAMj9MaeLpTeB2gyMn_ZGA41HxgoZcJD+WX6S2crZq=5OnC7jmg@mail.gmail.com"
type="cite">Cheers,<br>
Cuong <br>
<br>
<div class="gmail_quote">2012/5/1 Justin A. Lemkul <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb">
<div class="h5"><br>
<br>
On 4/30/12 10:02 PM, cuong nguyen wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs Users,<br>
<br>
I used the command "genbox -cs spc216.gro -o box1.g96 -p
topol.top -box 3 3 10"<br>
to create box of 3010 water molecules. However, now I
need to create a same size<br>
box with only 846 water molecules. Please help me to do
this.<br>
<br>
</blockquote>
<br>
</div>
</div>
Use the -maxsol option when invoking genbox.<br>
<br>
-Justin<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>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080" value="+15402319080"
target="_blank">(540) 231-9080</a><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================
<div class="HOEnZb">
<div class="h5"><br>
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</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<div>Nguyen Van Cuong</div>
<div>PhD student - Curtin University of Technology</div>
<div>Mobile: (+61) 452213981</div>
<div> </div>
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