[gmx-users] g_wham error
rajatdesikan at gmail.com
Sat Nov 19 19:20:13 CET 2011
Oh lovely...thanks for the quick reply Justin :)...
On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> rajat desikan wrote:
>> 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
>> 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 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
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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
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