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On 27/09/2011 12:49 PM, Liu, Liang wrote:
<blockquote
cite="mid:CABxJRo+D7kvJi6-K2-ECpm7g03nO-Lz7sH3YJwmwgjgO3vfoNQ@mail.gmail.com"
type="cite"><font color="#000099"><font face="verdana,sans-serif">Thanks.</font></font>
<div><font class="Apple-style-span" face="verdana, sans-serif"
color="#000099"><br>
</font></div>
<div><font class="Apple-style-span" face="verdana, sans-serif"
color="#000099">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.</span></div>
</blockquote>
<br>
"Always" is too strong, but this is common.<br>
<br>
<blockquote
cite="mid:CABxJRo+D7kvJi6-K2-ECpm7g03nO-Lz7sH3YJwmwgjgO3vfoNQ@mail.gmail.com"
type="cite">
<div><span class="Apple-style-span" style="font-family: Georgia,
serif; font-size: 16px; line-height: 20px; background-color:
rgb(255, 255, 255); "> Is it possible to fulfill the position
restraint during Position Restrained MD? Thanks.</span></div>
</blockquote>
<br>
Yes, hence the name. How well they can be fulfilled depends on the
initial and simulation conditions.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CABxJRo+D7kvJi6-K2-ECpm7g03nO-Lz7sH3YJwmwgjgO3vfoNQ@mail.gmail.com"
type="cite">
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<div class="gmail_quote">On Mon, Sep 26, 2011 at 4:56 PM,
Justin A. Lemkul <span dir="ltr"><<a
moz-do-not-send="true" 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>
<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080" value="+15402319080"
target="_blank">(540) 231-9080</a><br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
</blockquote>
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</div>
-- <br>
Best,<br>
Liang Liu<br>
</div>
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