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>

        ==============================__==========
-- 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>
        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 gmx-users-requ...@gromacs.org
        <mailto:gmx-users-requ...@gromacs.org>.
        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




--
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

========================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to