It seems that i cannot figure out a way to change the absolute reference point (Its the origin by default).<div><br></div><div>Amit<br><br><div class="gmail_quote">On Mon, Jan 17, 2011 at 5:52 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;"><div class="im"><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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>
</blockquote>
<br></div>
Correct.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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>
</blockquote>
<br></div>
Using a defined reference group is the better method. That way, the pull distance is calculated with respect to this reference, and it sounds like that will allow you to use the box you have already set up.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Thanks for looking into this.<br>
<br></div><div class="im">
On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Amit Choubey wrote:<br>
<br></div>
Hi,<div class="im"><br>
I am still not able to see the reason for the periodic distances<br>
coming into picture.<br>
<br>
<br>
I guess I don't fully understand your procedure. If you only want<br>
to pull to a COM separation of 15 nm, there should be no problem,<br>
but yet you're achieving a COM separation of 18.5 nm? That's<br>
exactly the problem. If your box is 37 nm, 18.5 nm corresponds to<br>
the transition at which the code utilizes either the unit cell<br>
distance or the periodic distance as the restraint distance. So it<br>
is as this point that your forces go haywire.<br>
<br>
-Justin<br>
<br>
Also, why pull_geometry = direction_periodic cannot be used with<br>
P-coupling; although it seems to do what i want.<br>
<br>
Amit<br>
<br>
On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey<br>
<<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>><br></div><div class="im">
<mailto:<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<br>
want to<br>
pull 15 nm. I started with a box size of 37 nm in the pull<br>
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<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<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> <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<br>
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<br>
reaches half<br>
the box length. The COM position changes by the box<br>
length<br>
and that causes huge force on the group. What should<br>
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<br>
periodic<br>
distance becomes the reference distance when this<br>
happens. This<br>
has been discussed numerous times on the list (hint:<br>
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>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> |<div class="im">
<br>
(540) 231-9080<br>
<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>
<br>
========================================<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
</div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><div><div></div>
<div class="h5"><br>
<br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a><br>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br>
<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<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>
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<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>
<br>
========================================<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
</div></div></blockquote><div><div></div><div class="h5">
<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>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br></div>