Re: [gmx-users] Re: Box-dimensions -g_energy_output

Justin A. Lemkul Fri, 24 Jun 2011 06:15:51 -0700


Kavyashree M wrote:

Sir.
I am sorry for changing the topic. It was not intentional
It just came as I wanted to mention the other part of the
problem that data had.

I'm trying to focus the discussion because you've presented three separate(maybe related) issues:


1. Wrong number of frames read
2. Wrong averages (in the case of box vectors)
3. Nonsensical standard deviations (in the case of temperature)

I have checked the entire file of the gmxdump output
of ener.edr firl for Box dimention as well as Temp.

If there's nothing suspicious, then try processing the file with g_energy from4.5.4; if that gives the same problem then we can rule out g_energy being atfault and the problem lies with the .edr file. But if you're saying thateverything is fine, then there's no clear solution. If I recall, you've saidother simulations you've done have given normal results. In that case, re-runthe simulation that's causing problems (or at least a short part of it, to test)and see if you get usable output.


-Justin

Thanks
With Regards
M. Kavyashree

On Fri, Jun 24, 2011 at 6:32 PM, Justin A. Lemkul <[email protected]<mailto:[email protected]>> wrote:




    Kavyashree M wrote:

        Sir,

        I went through the whole .edr file for one
        specific term in which I was getting nan.
        Of the three columns (Energy; Av. Energy; Sum Energy)
        order (power) for temperature did not change at all in the
        first column but in the second column there was a change of
        power between +1 and +2 which was +2 in another .edr file from
        other simulation.
        ven though the second column value is arround 1--e+02 while
        those with +1 power is around 9.--e+01 which is quite near to
        1.--e+02.

        But I did not find any huge changes in the temperature.


    Per my previous message, please focus on the issue at hand.  I do
    not recall the specifics of the issue with temperature and I'm not
    going to go digging through the archive for messages scattered over
    many days.  You started this thread regarding box vectors, for which
    we have the data below in the thread.  Please keep the discussion
    focused.  If you jump around between ideas with somewhat abstract
    descriptions, no one is going to be interested in troubleshooting.
     If you want free help, make it easy to help you.

    If you have something relevant to post regarding box vectors, please
    do so, otherwise, if you want to investigate a different issue
    please give it proper context (new thread or including information
    from the old thread).

    Actual output would be useful, although I realize that may be too
    large of a message to send across the list, so snippets that
    illustrate anything useful would be appropriate.

    -Justin

        Thank you
        With Regards
        M. Kavyashree

        On Fri, Jun 24, 2011 at 5:53 PM, Kavyashree M <[email protected]
        <mailto:[email protected]> <mailto:[email protected]
        <mailto:[email protected]>>> wrote:

           Sir,

           I tried it already but It was huge file. this kind of nan
        comes only
           for RMSD not for any other term. I will try looking into that
        file
           again.

           Thanks
           With regards
           M. Kavyashree




           On Fri, Jun 24, 2011 at 5:20 PM, Justin A. Lemkul
        <[email protected] <mailto:[email protected]>
           <mailto:[email protected] <mailto:[email protected]>>> wrote:



               Kavyashree M wrote:

                   Sir,

                   I am sorry I did not get any mail for that query since I
                   posted it.
                   So I had to ask once again..

                   1. g_energy -f ener.edr -o  box.xvg
                      selecting 15 16 17 0

                   2. gmxcheck -e ener.edr

                     Opened ener.edr as single precision energy file

frame: 0 (index 0), t: 0.000Lastenergy frame read 50000 time 100000.000Found 50001 frames with a timestep of 2 ps.


                   3. Gromacs version 4.5.3

                   This is the same data where I was mentioning that I
                   was getting "not a number"  (nan) error for all
                   energy calculations under RMSD section.


               I've said several times before that this energy file is
        probably
               junk, and again I'd suspect that.  The only thing to
        check would
               be to run gmxdump on the .edr file (and redirect into some
               output file or pipe the output through "more" to actually see
               it) and see where the energy values go screwy.  If you find a
               bunch of nonsensical information, then you have your answer.

               -Justin

                   Thank you fro answering.

                   With Regards
                   M. Kavyashree


                   On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul
                   <[email protected] <mailto:[email protected]>
        <mailto:[email protected] <mailto:[email protected]>>
                   <mailto:[email protected] <mailto:[email protected]>
        <mailto:[email protected] <mailto:[email protected]>>>> wrote:



                      Kavyashree M wrote:

                          Dear users,

                          Any suggestions?


                      You haven't provided nearly enough diagnostic
        information
                   for anyone
                      to offer you any useful help (as Mark said yesterday).
                    For example,
                      please provide:

                      1. Your exact g_energy command line
                      2. The output of gmxcheck for this .edr file
                      3. Your Gromacs version

                      -Justin

                          Thank you
                          M. Kavyashree


                          On Thu, Jun 23, 2011 at 10:38 AM, Kavyashree M
                          <[email protected] <mailto:[email protected]>
        <mailto:[email protected] <mailto:[email protected]>>
                   <mailto:[email protected] <mailto:[email protected]>
        <mailto:[email protected] <mailto:[email protected]>>>
                          <mailto:[email protected]
        <mailto:[email protected]> <mailto:[email protected]
        <mailto:[email protected]>>
                   <mailto:[email protected] <mailto:[email protected]>
        <mailto:[email protected] <mailto:[email protected]>>>>> wrote:

                             Dear users,

                              In one of the simulations while
        calculating box
                   dimensions
                             using g_energy this output was obtained -
                             Statistics over 50000001 steps [ 0.0000 through
                   100000.0000
                          ps ], 3
                             data sets
                             All statistics are over 1978700 points

Energy AverageErr.Est. RMSD

                           Tot-Drift

------------------------------______--------------------------__--__--__-------------------Box-X 0.04532291.8 0.637535 -9.93022 (nm)Box-Y 0.04532291.8 0.637535 -9.93022 (nm)Box-Z 0.03204821.3 0.450805 -7.02173 (nm)


                             but the dimensions of the box is different.
        plot
                   attached.
                             I am not able to figure out why only
        1978700 data
                   point are
                          considered.
                             Kindly give some suggestions.

                             Thank you
                             with regards
                             M.Kavyashree



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

                      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> |

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

               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>>

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--==============================__==========


    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>

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

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] Re: Box-dimensions -g_energy_output

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