rajat desikan wrote:
hi Justin
I am not able to tell where the lack of overlap is. This is the first
wham plot I am looking at. In your tutorial and literature, the wham
plots are so clear. Can you please help me? Thanks.
It looks like your first one or two windows were not restrained sufficiently at
the desired distance. The error complains that bin 2 should have points at
0.366 nm, but it appears neither bin 1 nor bin 2 satisfy this requirement.
Check carefully what you have set for reference distances and what distances
were actually maintained during the sampling. You may need a stronger restraint
or longer simulations. How long are the simulations? I see that you're
starting the analysis on data after 2 ns, but how much does that leave?
-Justin
On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan <rajatdesi...@gmail.com
<mailto:rajatdesi...@gmail.com>> wrote:
Oh lovely...thanks for the quick reply Justin :)...
On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
rajat desikan wrote:
Hi
I am a new gromacs user. I just completed Justin's umbrella
sampling tutorial. I am doing a PMF calculation between 2
methane molecules in water. The simulation has run fine till
the g_wham step. My command is
-- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist
-unit kCal -b 2000
I get a warning:
WARNING, no data point in bin 2 (z=0.366256) !
You may not get a reasonable profile. Check your histograms!
and my histogram contains a single peak.
I have pulled my other methane 1 nm away from the first
methane. I have 15 sampling windows (0.05 nm apart till 5nm
and then 1 nm apart)...can you please tell me how to correct
this?
With 15 windows, you should have 15 histograms. Plot with:
xmgrace -nxy histo.xvg
It will show you where the lack of sampling is.
-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>
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--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
------------------------------------------------------------------------
--
========================================
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
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