shahid nayeem wrote:
Dear Justin
I did some more sampling and sending you profile.xvg, histo.xvg. and
hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell
my the difference in profile.xvg and hist.xvg. Both should be same but I
get different curves here.
I can't tell you the difference because you haven't shown how they were
generated. My blind guess is that hist.xvg (a very confusing name for a PMF
profile) was generated from data that have poor sampling in two regions. The
contents of profile.xvg look normal. I don't know which of these curves
corresponds to histo.xvg, because the histograms therein look fine.
Please make sure to give full descriptions of these files. You've quote a
message that is over a month old. I've replied to hundreds of messages since
then and I do not remember the full context of our discussion.
-Justin
On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
shahid nayeem wrote:
Dear Justin
I did pmf calculation for my protein-protein complex using your
tutorial.Off course changing the pull_direction suitable for my
protein but more or less following the same strategy. I am using
gromacs_4.5.4 and g_wham utility. The profile.xvg file which I
get is attached and it shows two dips in PE curve. Please see it
and tell me why I am getting these dips.
You have insufficient sampling in at least these two regions. Your
histograms should confirm this.
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
