Thanks a lot to both of you.<br><br>Chitrita.<br><br><div class="gmail_quote">On Wed, Mar 11, 2009 at 2:09 AM, 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>
Chitrita Dutta Roy 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 Tsjerk,<br>
<br>
Did you mean to send you the md.mdp file that I used to run grompp for md simulation? I am using Gromacs 4.0.2 versision. I am not very clear about the parameters used in mdp files. So I am sending the mdp file here.<br>
<br>
</blockquote>
<br></div>
Some consultation with the manual will provide you with the information to learn about these parameters. They should not be set blindly!<br>
<br>
> cpp = /usr/bin/cpp<br>
<br>
This is an example of one of the obsolete parameters no longer used in Gromacs 4.0.x, hence grompp told you it would be ignored.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Tcoupl = V-rescale<br>
tau_t = 0.1 0.1<br>
tc_grps = Protein SOL<br>
ref_t = 300 300<br>
</blockquote>
<br></div>
Here is the problem, as grompp pointed out to you. You are controlling the temperature of both the Protein and solvent water (SOL). But your system contains NA+, doesn't it? So it is not part of any temperature coupling group. Try "Protein Non-Protein" for simple aqueous systems with ions.<br>
<font color="#888888">
<br>
-Justin</font><div class="im"><br>
<br>
-- <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>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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