Dear Dr.Justin<br><br>Thank you for your reply<br>My is Protein-ligand,It is have the same conditions as tutorial.I did pull ligand in the z direction.<br>Actualy I found your note about gen_vel ,but I didn't any about Continuation!<br>
<br>You are right,But there is another problem:<br>You have not used any -t option in grompp command (doing umbrella step).<br><br>Since we have set Continuation=yes;<br>Can grompp realize from which .cpt (npt.cpt ) it must use ?<br>
<br>And my last question:<br>Do I need to any .cpt file ? (Because I have set Continuation=yes)<br><br>Thanks in advance <br><br><br><br><br><br><br><div class="gmail_quote">On Mon, May 2, 2011 at 3:27 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>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Dr.Justin<br>
<br>
Regarding Umbrella Sampling tutorial:<br>
<br>
The CONTINUATION option in md_umbrella.mdp is YES,<br>
and you have noticed : From NPT<br>
<br>
I can't understand it's reason correctly!<br>
<br>
</blockquote>
<br></div>
This is a meaningless comment. It was left there from copying and pasting files before modifying them. The important part is that "continuation = yes" be set to correctly solve the constraints.<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;">
we run a NPT and then Pulling, then extracted some configurations from pull.trr file.<br>
I think we must continue from pull.cpt not NPT.cpt<br>
<br>
I mean :<br>
grompp -f md_umbrella.mdp ............................. -t pull.cpt is more correct than<br>
<br>
grompp -f md_umbrella.mdp .............................. -t NPT.cpt<br>
<br>
am I right?<br>
</blockquote>
<br></div>
In the case of the tutorial, no. There is not a corresponding .cpt file for each configuration generated. If you were to somehow apply the same .cpt file for each configuration, almost certainly some of the windows would blow up because the initial velocities would cause nasty collisions. Note that I discuss the continuation issue, proper settings for gen_vel, etc. in the tutorial, step six.<br>
<br>
-Justin<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;">
Thanks in advance for your reply<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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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