shahid nayeem wrote:
Both files hist.xvg and profile.xvg both are simultaneous output of this
command. I did not run it twice, once to get profile.xvg and then to get
hist.xvg as you uderstood.
They cannot be simultaneous output. The file named "hist.xvg" contains a PMF
profile and has a date stamp of July 5 (in the .xvg header). The file
"profile.xvg" is also a PMF profile and a has a date of August 11. They were
not produced simultaneously. The file "histo.xvg" (with which you may be
confusing "hist.xvg") was produced alongside "profile.xvg" and contains the
umbrella sampling histograms, and was produced alongside "profile.xvg."
I think you've somehow lost track of which files are which. It seems that
"hist.xvg" contains the PMF profile from poor sampling, per our discussion a
month ago, and "profile.xvg" contains something newer, likely with better data.
-Justin
On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
shahid nayeem wrote:
I used following command
g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist
-unit kCal
Both profile.xvg and hist.xvg are created with this command
using same pullf.xvg and .tpr files.
An identical command with identical input files producing totally
different output? Sorry, but I find that hard to believe. Check
your work and make sure you're using the input you think you are. I
suspect something's amiss and you're not seeing it.
-Justin
shahid Nayeem
On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
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>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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> <http://vt.edu>
<http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.______vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<http://vt.edu/Pages/Personal/__justin
<http://vt.edu/Pages/Personal/justin>>
<http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<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>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto: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>
<http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>>
<http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<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>
<http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>>
<http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>
<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>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-request@
<mailto:gmx-users-request@>__gr__omacs.org <http://gromacs.org>
<mailto:gmx-users-request@__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>
<http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>>
<http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>
<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 <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
<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>
<mailto: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>
<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>
<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>
<mailto:gmx-users-request@__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>
<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 <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
