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On 23/01/2012 9:27 PM, priya thiyagarajan wrote:
<blockquote
cite="mid:CAEuVTxCTXYmj_zpVGFKPC_+i3qO2UisAgk+PYrDva5HTQuAh6w@mail.gmail.com"
type="cite">hello sir,<br>
<br>
i like to know few informations regarding box dimension and
setting no.of.solvent molecules..<br>
<br>
i want to run simulation for different number of protein molecules
with same number of water molecules..<br>
i used following commands <br>
to increase the no.of molecules i used <br>
genbox -nmol 100 -ci protein.pdb -box 15 15 15 -o protein100.pdb<br>
<br>
then i set box type<br>
<br>
editconf -f protein100.pdb -bt cubic -o prot100_box.pdb
-box 15 15 15 <br>
<br>
to add water <br>
<div style="text-align:center"><br>
</div>
<br>
<p class="MsoNormal">genbox -cp prot100_box.pdb -cs spc216.gro -p
topol.top -o prot100_water.pdb -maxsol 50000 </p>
<p class="MsoNormal"><br>
</p>
<p class="MsoNormal"><br>
</p>
<p class="MsoNormal">when i added 50000 water molecules only half
of my box is getting filled by solvent molecules..</p>
</blockquote>
<br>
Go and work out how many water molecules at normal density you can
have in a 15nm^3 box.<br>
<br>
Mark<br>
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