Yes Justin i understand that. Heres what i think is going on<br><br>I dont have any reference group. Now the COM distance is calculated wrt the origin and whenever the COM is more than half of the box its causing problem. <br>
<br>I think changing the absolute reference to the initial COM of the pull group (using pull_init1) should fix this issue but i am not confident.<br><br>Thanks for looking into this.<br><br><div class="gmail_quote">On Mon, Jan 17, 2011 at 5:36 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi, <br>
I am still not able to see the reason for the periodic distances coming into picture.<br>
<br>
</blockquote>
<br></div>
I guess I don't fully understand your procedure. If you only want to pull to a COM separation of 15 nm, there should be no problem, but yet you're achieving a COM separation of 18.5 nm? That's exactly the problem. If your box is 37 nm, 18.5 nm corresponds to the transition at which the code utilizes either the unit cell distance or the periodic distance as the restraint distance. So it is as this point that your forces go haywire.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
Also, why pull_geometry = direction_periodic cannot be used with P-coupling; although it seems to do what i want.<br>
<br>
Amit<br>
<br></div><div class="im">
On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey <<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a> <mailto:<a href="mailto:kgp.amit@gmail.com" target="_blank">kgp.amit@gmail.com</a>>> wrote:<br>
<br>
Hi,<br>
<br>
Initially, the pull group center of mass is at 8.16 nm and i want to<br>
pull 15 nm. I started with a box size of 37 nm in the pull direction. <br>
The problem occurs when the COM is at 18.5 nm (ie at half the box<br>
length).<br>
<br>
Thanks for the attention.<br>
<br>
Amit<br>
<br>
On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Amit Choubey wrote:<br>
<br>
Hi all,<br>
<br>
I am trying to do pulling simulation. Following are the pull<br>
parameters<br>
<br>
pull = umbrella<br>
pull_geometry = direction<br>
pull_vec1 = 0 0 1<br>
pull_group1 = RNA<br>
pull_rate1 = 0.01<br>
pull_k1 = 1000<br>
pull_start = yes<br>
<br>
Everything works fine until the pull group COM reaches half<br>
the box length. The COM position changes by the box length<br>
and that causes huge force on the group. What should i do to<br>
fix this ? Also i am using NPT coupling.<br>
<br>
<br>
You have to use a sufficiently large box, otherwise the periodic<br>
distance becomes the reference distance when this happens. This<br>
has been discussed numerous times on the list (hint: there is an<br>
archive for a reason!) and in the tutorial linked here:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling" target="_blank">http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling</a><br>
<br>
-Justin<br>
<br>
Amit<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>
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<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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