Hi, <div><br></div><div>I am still not able to see the reason for the periodic distances coming into picture.</div><div><br></div><div>Also, why <span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">pull_geometry = direction_periodic cannot be used with P-coupling; although it seems to do what i want.</span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Amit<br>
</span></font><br><div class="gmail_quote">On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey <span dir="ltr"><<a href="mailto:kgp.amit@gmail.com">kgp.amit@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi,<div><br></div><div>Initially, the pull group center of mass is at 8.16 nm and i want to pull 15 nm. I started with a box size of 37 nm in the pull direction. </div><div><br></div><div>The problem occurs when the COM is at 18.5 nm (ie at half the box length).</div>
<div><br></div><div>Thanks for the attention.</div><div><br></div><font color="#888888"><div>Amit</div></font><div><div></div><div class="h5"><div><br></div><div><div class="gmail_quote">On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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"><div><div></div><div><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I am trying to do pulling simulation. Following are the pull 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 the box length. The COM position changes by the box length and that causes huge force on the group. What should i do to fix this ? Also i am using NPT coupling.<br>
<br>
</blockquote>
<br></div></div>
You have to use a sufficiently large box, otherwise the periodic distance becomes the reference distance when this happens. This has been discussed numerous times on the list (hint: there is an 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>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Amit<br>
<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 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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</div></div></blockquote></div><br></div>