Justin, Should i turn off charges on the methane molecules? I have left them on.
On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul <[email protected]> wrote: > > > rajat desikan wrote: > >> My simulations are for 10 ns in each window. There is a lot of noise in >> my wham too. I am enclosing my wham for pullf (the earlier was pullx) and >> pmf. They are really looking strange. Stronger restraint means force >> constant? >From literature, I kept it at 3000. >> >> > Those plots do look very strange. The PMF is almost a step function, > which is certainly wrong. You may need either more simulation time or more > frequent collection of data points, but at this stage I can only guess. > Not much more I can offer, sorry. > > A stronger restraint would mean a stronger force constant, yes, but if > you're using 3000 to restrain simple molecules like methane, I think there > is no need to increase it. > > -Justin > > On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> 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 >> <[email protected] <mailto:[email protected]**> >> <mailto:[email protected] >> >> <mailto:[email protected]**>__>> wrote: >> >> Oh lovely...thanks for the quick reply Justin :)... >> >> >> On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[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 <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://www.bevanlab.biochem._**_ >> 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 >> [email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected] >> >**> >> >> 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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> > >> <mailto:gmx-users-request@__gr**omacs.org<http://gromacs.org> >> >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >>. >> 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> >> >> >> >> >> >> >> -- 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 <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 [email protected] >> <mailto:[email protected]> >> >> 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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >. >> 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> >> > >> >> >> >> >> -- >> 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<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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