There is a log attached in the first e-mail. <br>My first reaction was the same. Why 14 :).<br>Marius<br><br><br><div class="gmail_quote">On Mon, Apr 6, 2009 at 1:10 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im"><br>
<br>
Pawan Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
You should add 14 cl ions.<br>
</blockquote>
<br></div>
Why 14? The number of Cl- ions that are necessary is pretty much spelled out by grompp, and the net charge of the system is printed in the .top (qtot section in [atoms]). If your system has a net charge of +2, add 2 Cl- ions, and so forth.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Regards,<br>
Pawan<div class="im"><br>
<br>
On Mon, Apr 6, 2009 at 12:26 PM, akalabya bissoyi <<a href="mailto:bissoyi.akalabya@gmail.com" target="_blank">bissoyi.akalabya@gmail.com</a> <mailto:<a href="mailto:bissoyi.akalabya@gmail.com" target="_blank">bissoyi.akalabya@gmail.com</a>>> wrote:<br>
<br>
hello gromacs<br>
i am trying to minimise my protein-ligand complex in gromacs.but it<br>
shows that system has non zero charge<br>
can any body says how much *cl ion*, i have to add to neutralised<br>
it. i am terminal window text.<br>
thank u<br>
-- AKALABYA BISSOYI<br>
N.I.T.Rourkela<br>
<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<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>
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