Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul <[email protected]> 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 | (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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- 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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