Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple of doubts Justin. Since, I am pulling the methane away steadily, it should smoothly increase the distance right? But the second methane molecule is both increasing and decreasing it's position, sort of going back and forth. Also, one more thing. Originally, I had given the option for pull_dim as Y N N (x direction). But the second methane moved in all 3 directions. So I position restrained the second methane to the x axis (Fcx=0, Fcy=1000 and Fcz=1000)...does this have any bearing on my simulations?
On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > rajat desikan wrote: > >> Justin, >> Should i turn off charges on the methane molecules? I have left them on. >> >> > What force field are you using? If you've got an all-atom model of > methane, you should have partial charges. > > -Justin > > On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> 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 >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> 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 >> <rajatdesi...@gmail.com <mailto:rajatdesi...@gmail.com**> >> <mailto:rajatdesi...@gmail.com <mailto:rajatdesi...@gmail.com** >> >__> >> <mailto:rajatdesi...@gmail.com >> <mailto:rajatdesi...@gmail.com**> >> >> <mailto: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> >> <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: >> >> >> >> 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> >> <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://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://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 >> 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> >> >> >> >> >> <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> >> >> >> >> >> <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. 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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 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. 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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 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. 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