<div dir="ltr">Thanks for you prompt reply! Clear and to the point.<br>-Shay<br><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 2:03 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<br>
Shay Teaching wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Gromacs Users,<br>
<br>
I've done Justin's tutorial regarding PMF/umbrella sampling and now, when approaching my own system I have a couple of questions.<br>
(Link to the tutorial here: <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin/<u></u>gmx-tutorials/umbrella/06_<u></u>umbrella.html</a> )<br>
<br>
My system is comprise of a transport protein (embedded in membrane) and a ligand. The system is positions so that Z axis is the axis on which I've made PMF windows.<br>
The next step on this is to run these windows separately and I didn't quite understand why in step-6 of the tutorial it specifies to still use pull_dim = N N Y and pull_rate1 = 0.0.<br>
<br>
As far as I understood, during the production run we want to sample the Z position. Shouldn't then it use pull_dim = Y Y N ?<br>
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No, that would confine the pulled group to the x-y plane, but allow it to move freely in z.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
And what does it mean to the system when we set pull_rate1 = 0.0 ?<br>
</blockquote>
<br></div>
The harmonic restraint is applied to pull_group1 such that there is no net change in position.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Does it mean that when pull_dim = N N Y and pull_rate1 = 0.0 it restrains pull_group0 on the Z-axis?<br>
<br>
</blockquote>
<br></div>
Not pull_group0 (which is the reference group), but pull_group1. Otherwise, yes.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
This came a bit longish,<br>
Thanks in advance,<br>
<br>
-Shay<br>
<br>
P.S.<br>
Using Gromacs 4.0.7<br>
<br>
<br>
<br>
</blockquote>
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<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<div class="im"><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>
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==============================<u></u>==========<br>
-- <br></div>
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