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

               <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://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

------------------------------------------------------------------------


------------------------------------------------------------------------


--
========================================

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