Re: [gmx-users] g_wham error

Justin A. Lemkul Sun, 20 Nov 2011 14:09:39 -0800


rajat desikan wrote:

Sorry, sorry...I have used Opls AA. The methane was going back and forthin the pulling during which I generated the configurations.

Assuming you used a harmonic potential, that is to be expected. As long as youhave set up reasonable spacing for your sampling windows from the snapshotsalong that trajectory, that should not be an issue. I also see no reason foruneven spacing in a system as simple as this one, though that's not a problem,per se, just not necessary.


-Justin

On Mon, Nov 21, 2011 at 3:28 AM, Justin A. Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote:




    rajat desikan wrote:

        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


    This is fundamentally incorrect.  53A6 is a united-atom force field,
    so each methane should be a single particle with 0 charge using the
    CH4 atom type.


        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.


    This sounds like SMD, not umbrella sampling.  Or are you referring
    to the pulling during which you generated configurations for
    umbrella sampling?


        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.


    There is no reason to suppose that pulling in only one dimension
    will necessarily be correct.  The dissociation of two simple
    molecules can occur in 3 dimensions.


        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?


    It should be unnecessary to restrain either molecule.

    -Justin

        On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto: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>
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        <mailto: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>
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        <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
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                                Oh lovely...thanks for the quick reply
        Justin :)...


                                On Sat, Nov 19, 2011 at 10:57 PM, Justin
        A. Lemkul
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                                    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
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                                    Department of Biochemistry
                                    Virginia Tech
                                    Blacksburg, VA
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                             --         Rajat Desikan (Ph.D Scholar)
                             Prof. K. Ganapathy Ayappa's Lab (no 13),
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------------------------------________------------------------__--__--__--__------------

--==============================________==========


                         Justin A. Lemkul
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                      --         Rajat Desikan (Ph.D Scholar)
                      Prof. K. Ganapathy Ayappa's Lab (no 13),
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------------------------------______--------------------------__--__--__------------



                  --     ==============================______==========

                  Justin A. Lemkul
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               --         Rajat Desikan (Ph.D Scholar)
               Prof. K. Ganapathy Ayappa's Lab (no 13),
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               Indian Institute of Science, Bangalore


           --     ==============================____==========

           Justin A. Lemkul
           Ph.D. Candidate
           ICTAS Doctoral Scholar
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           Department of Biochemistry
           Virginia Tech
           Blacksburg, VA
           jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
        231-9080
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--Rajat Desikan (Ph.D Scholar)

        Prof. K. Ganapathy Ayappa's Lab (no 13),
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        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
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--
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

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