Thank you for your detailed axplain<br>I understood completely<br><br><div class="gmail_quote">On Mon, May 2, 2011 at 4:34 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 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>
</div></blockquote>
<br>
Not that specific keyword, no, but I do address the general principle about continuing these simulations via this very discussion about gen_vel.<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;">
You are right,But there is another problem:<br>
You have not used any -t option in grompp command (doing umbrella step).<br>
<br>
</blockquote>
<br></div>
Correct. See the discussion on gen_vel that I referenced earlier.<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;">
Since we have set Continuation=yes;<br>
Can grompp realize from which .cpt (npt.cpt ) it must use ?<br>
<br>
</blockquote>
<br></div>
grompp does not make any choice about what it should use. It takes whatever input you give it and assembles a run input file. If you're following my procedure (which may or may not necessarily be applicable in all cases), then there will NOT be a suitable .cpt file for each starting configuration. These configurations were generated using SMD, and .cpt files are not written and saved at every frame so you have a corresponding one later.<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;">
And my last question:<br>
Do I need to any .cpt file ? (Because I have set Continuation=yes)<br>
<br>
</blockquote>
<br></div>
Checkpointing and continuation are related, but not identical. The "continuation" keyword deals with whether or not constraints are solved before the first integration step. It otherwise has nothing to do with the thermodynamic state of the system, which is contained in the .cpt file.<br>
<br>
For your system, as I state in the tutorial, you may want to set "gen_vel = yes" in each window (since there is no prior equilibration, which may be a problem for some systems, but not the tutorial example). This would eliminate the need for a .cpt file.<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;">
Thanks in advance <br><div><div></div><div class="h5">
<br>
<br>
<br>
<br>
<br>
On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
mohsen ramezanpour wrote:<br>
<br>
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>
<br>
This is a meaningless comment. It was left there from copying and<br>
pasting files before modifying them. The important part is that<br>
"continuation = yes" be set to correctly solve the constraints.<br>
<br>
<br>
we run a NPT and then Pulling, then extracted some<br>
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<br>
NPT.cpt<br>
<br>
am I right?<br>
<br>
<br>
In the case of the tutorial, no. There is not a corresponding .cpt<br>
file for each configuration generated. If you were to somehow apply<br>
the same .cpt file for each configuration, almost certainly some of<br>
the windows would blow up because the initial velocities would cause<br>
nasty collisions. Note that I discuss the continuation issue,<br>
proper settings for gen_vel, etc. in the tutorial, step six.<br>
<br>
-Justin<br>
<br>
<br>
Thanks in advance for your reply<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>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
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</div></blockquote><div><div></div><div class="h5">
<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>
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>
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