<span style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows.</span><div style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<div>; Pull code</div><div>pull = umbrella</div><div>pull_geometry = distance ; simple distance increase </div><div>pull_dim = Y N Y</div><div>pull_vec1 = 0.75 0 1</div><div>pull_start = yes ; define initial COM distance > 0</div>
<div>pull_ngroups = 1</div><div>pull_group0 = Chain_B </div><div>pull_group1 = Chain_A </div><div>pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns</div><div>pull_k1 = 1000 ; kJ mol^-1 nm^-2</div>
<div><br></div><div>Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence.</div><div>Shahid Nayeem</div></div><br><div class="gmail_quote">On Mon, Feb 20, 2012 at 10:48 PM, shahid nayeem <span dir="ltr"><<a href="mailto:msnayeem@gmail.com">msnayeem@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows.<div>
<div>; Pull code</div><div>pull = umbrella</div><div>pull_geometry = distance ; simple distance increase </div>
<div>pull_dim = Y N Y</div><div>pull_vec1 = 0.75 0 1</div><div>pull_start = yes ; define initial COM distance > 0</div><div>pull_ngroups = 1</div><div>pull_group0 = Chain_B </div><div>
pull_group1 = Chain_A </div><div>pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns</div><div>pull_k1 = 1000 ; kJ mol^-1 nm^-2</div><div><br></div><div>Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence.</div>
<div>Shahid Nayeem</div><div><div></div><div class="h5"><br><div class="gmail_quote">On Mon, Feb 20, 2012 at 8:24 PM, 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><br>
<br>
shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks Justin<br>
I have pulled one of the chain from an initial COM distance value of 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the <br>
</blockquote>
<br></div>
I will have to assume you mean nm. Gromacs does not deal in Angstrom, and these distances would be within any sensible short-range cutoff and thus not indicative of actual separation.<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
chain is completely separated. But even at this separation the profile.xvg file does not show its convergence to one value. I sent this file to you earlier.<br>
</blockquote>
<br></div>
Sorry, I don't have a photographic memory, nor can I recall if you've ever posted your .mdp file, or at the very least, told us how much sampling you've done in each window. It may well be that your simulations are simply too short to observe adequate post-equilibration sampling.<div>
<div></div><div><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<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/<u></u>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/<u></u>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/<u></u>Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br></div></div></div>
</blockquote></div><br>