<font color="#000099"><font face="verdana,sans-serif">Thanks.</font></font><div><font class="Apple-style-span" color="#000099" face="verdana, sans-serif"><br></font></div><div><font class="Apple-style-span" color="#000099" face="verdana, sans-serif">Is this position restraint same to the one "</font><span class="Apple-style-span" style="font-family: Georgia, serif; font-size: 16px; line-height: 20px; background-color: rgb(255, 255, 255); ">Position Restrained MD</span><span class="Apple-style-span" style="color: rgb(0, 0, 153); font-family: verdana, sans-serif; ">". I see some tutorial shows there are always three step to perform a simulation: </span><span class="Apple-style-span" style="font-family: Georgia, serif; font-size: 16px; line-height: 20px; background-color: rgb(255, 255, 255); ">Energy minimization, </span><span class="Apple-style-span" style="font-family: Georgia, serif; font-size: 16px; line-height: 20px; background-color: rgb(255, 255, 255); ">Position Restrained MD and </span><span class="Apple-style-span" style="font-family: Georgia, serif; font-size: 16px; line-height: 20px; background-color: rgb(255, 255, 255); ">MD Simulation. Is it possible to fulfill the position restraint during Position Restrained MD? Thanks.</span></div>
<div><div><br><div class="gmail_quote">On Mon, Sep 26, 2011 at 4:56 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Liu, Liang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Firstly I want to thank for your reply, yes, it should be position restraint.<br>
<br>
I don't know how to reply in the thread, actually that was my first post. Therefore I have to ask you here, hope it also work to you.<br>
<br>
</blockquote>
<br>
Simply reply to the message. The discussion needs to stay on the list. The members are not private tutors.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
My question is how to perform a position restraint simulation with the heavy atom constrained to its initial position by a harmonic potential E=k(r-r0)^2,<br>
which changes with k equal to 0, 10, 20, ..., 90, 100, and so on?<br>
<br>
</blockquote>
<br>
You can adjust the force constant in the posre.itp file. There is no automated way of decreasing or increasing a restraint; independent simulations must be run on the different topologies.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks, and any helps will be highly appreciated.<br>
<br>
-- <br>
Best,<br>
Liang Liu<br>
</blockquote>
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-- <br>
==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Liang Liu<br>
</div></div>