hi Justin,<br>Thanks for your reply...<br>I am interested in looking for the stability of the docked pose, by applying some temperature variation in the molecule.<br>If I am applying temperature variation then should I use pressure coupling simultaneously.<br>
Can you suggest some tutorial for such attempts.....<br><br>With Thanks,<br>Vivek<br><br><div class="gmail_quote">2008/11/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><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="Ih2E3d"><br>
<br>
vivek sharma 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 There,<br>
I am running MDS over the docked poses to check the stability of the docked poses using gromacs.<br>
I have few doubts about selecting parameters for the same, If anybody have tried such thing earlier, please suggest me for the same.<br>
<br>
Should I keep pressure coupling over the simulation ?<br>
</blockquote>
<br></div>
Sure; life exists at NPT, so it is commonly used in routine protein simulations.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
For how long should I run the simulation for such purpose ?<br>
<br>
</blockquote>
<br></div>
That's up to you :) You should run the simulations as long as you feel necessary to achieve stability. I know that's vague, but there really is no single correct answer to this question in the MD field. If there is, I'd love for someone to tell me, too...;)<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;"><div class="Ih2E3d">
Waiting for suggestions.<br>
<br>
With Thanks,<br>
Vivek<br>
<br>
<br></div>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<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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