Hello, <br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
The set pressure should reflect whatever system you are trying to model.<br></blockquote><div><br>This statement is not very clear to me.. But when the mdout.mdp file after grompp <br>during energy minimization is examined it says -<br>
<br>gen-vel = no<br>gen-temp = 300<br>gen-seed = 173529<br><br>Even though I have not assigned any velocities in em.mdp file. Thats the<br>reason why got this doubt about temperature during energy minimization.<br>
<br>Thank you<br>With Regards<br>Kavya<br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Thank you<br>
With Regards<br>
Kavya<br>
<br></div><div class="im">
On Mon, Oct 17, 2011 at 3:29 PM, bipin singh <<a href="mailto:bipinelmat@gmail.com" target="_blank">bipinelmat@gmail.com</a> <mailto:<a href="mailto:bipinelmat@gmail.com" target="_blank">bipinelmat@gmail.com</a>>> wrote:<br>
<br>
As far as I know we do energy minimization at room temperature only.<br>
Only during equilibration<br>
(NVT and NPT) we use high temperature for maintaining proper density<br>
before starting the final production run.<br>
<br>
On Mon, Oct 17, 2011 at 15:15, Kavyashree M <<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>>> wrote:<br>
> Dear users,<br>
><br>
> For simulating a protein at high temperature (more than 300K,<br>
> less than 400K) using OPLSAA forcefield, what are the parameters<br>
> other than Temperature that need to be taken care of?<br>
> Does the energy minimization step also needs to be done at high<br>
> temperature? (here my aim is not to simulate an unfolding event)<br>
> I have a reference -<br>
> Biophysical Journal Volume 94 June 2008 4444–4453<br>
><br>
> Any other references or suggestions will be helpful.<br>
><br>
> Thanking you<br>
> With Regards<br>
> M. Kavyashree<br>
><br>
><br>
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==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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