Thank you very much<br>I understood completely<br>Best<br><br><div class="gmail_quote">On Sun, May 8, 2011 at 7:30 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;"><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><div class="im">
Thank you for your complete explanation.<br>
Please let me discribe where is NPT.cpt comes from:<br>
<br>
Before doing Pulling step,I did an NPT step (as your tutorial) to generate NPT ensemble.<br>
the outputs of this step were NPT.cpt, NPT.gro and NPT.enr and ...<br>
<br>
Then I used NPT.gro for Pulling step to generate config0.gro and ...<br>
<br>
After this step I used the NPT.cpt and config0.gro and .... to generate umbrella0.tpr with grompp.<br>
I think it is obvious now ,where is NPT.cpt come from!<br>
<br>
I think my mistake is as you noted.I didn't use any -t option in grompp,Then I lost the information for npt ensemble.<br>
<br>
What do you think<br>
</div></blockquote>
<br>
The pre-SMD NPT ensemble has nothing to do with any of the configurations generated during SMD. The coordinates and ensemble information in NPT.cpt reflect the position-restrained system prior to the application of the steering force.<br>
<br>
You should not use this NPT.cpt file for anything after SMD. I explained an appropriate workflow in my last message.<div class="im"><br>
<br>
-Justin<br>
<br>
-- <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></div><div><div></div><div class="h5">
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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