Re: [gmx-users] g_wham error

Justin A. Lemkul Sun, 20 Nov 2011 13:59:57 -0800


rajat desikan wrote:

Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on thehydrogens...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 eachmethane should be a single particle with 0 charge using the CH4 atom type.

of doubts Justin. Since, I am pulling the methane away steadily, itshould smoothly increase the distance right? But the second methanemolecule is both increasing and decreasing it's position, sort of goingback and forth.

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

Also, one more thing. Originally, I had given the option for pull_dim asY 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 willnecessarily be correct. The dissociation of two simple molecules can occur in 3dimensions.

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>> 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>
        <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>
        <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 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
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        <mailto:rajatdesi...@gmail.com>__>__>
                      <mailto:rajatdesi...@gmail.com
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               <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>>
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                         <mailto:jalem...@vt.edu
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               <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
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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
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                  Virginia Tech
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------------------------------____----------------------------__--__------------



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

           Justin A. Lemkul
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           Virginia Tech
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--==============================__==========


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    Ph.D. Candidate
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    Virginia Tech
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    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Rajat Desikan (Ph.D Scholar)
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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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Re: [gmx-users] g_wham error

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