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

Kavyashree M hmkvsri at gmail.com
Fri Jun 24 15:09:04 CEST 2011


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

Thanks
With Regards
M. Kavyashree


On Fri, Jun 24, 2011 at 6:32 PM, Justin A. Lemkul <jalemkul at vt.edu> 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 <hmkvsri at gmail.com <mailto:
>> hmkvsri at gmail.com>> 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 <jalemkul at vt.edu
>>    <mailto:jalemkul at vt.edu>> 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:      0.000          Last
>>            energy frame read 50000 time 100000.000
>>  Found 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
>>            <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>            <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> 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
>>                   <hmkvsri at gmail.com <mailto:hmkvsri at gmail.com>
>>            <mailto:hmkvsri at gmail.com <mailto:hmkvsri at gmail.com>>
>>                   <mailto:hmkvsri at gmail.com <mailto:hmkvsri at gmail.com>
>>            <mailto:hmkvsri at gmail.com <mailto:hmkvsri at gmail.com>>>> 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                      Average   Err.Est.
>>            RMSD
>>                    Tot-Drift
>>                                        ------------------------------**
>> ____--------------------------**--__--__-------------------
>>                      Box-X                     0.0453229        1.8
>>        0.637535             -9.93022  (nm)
>>                      Box-Y                     0.0453229        1.8
>>        0.637535             -9.93022  (nm)
>>                      Box-Z                     0.0320482        1.3
>>        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> |
>>
>>            (540) 231-9080
>>
>>                          http://www.bevanlab.biochem.__**__
>> vt.edu/Pages/Personal/justin
>>            <http://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >>
>>
>>               ==============================**____==========
>>               --     gmx-users mailing list    gmx-users at gromacs.org
>>            <mailto:gmx-users at gromacs.org>
>>               <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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>
>> >
>>               <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>
>> >
>>               <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-request at gromacs.org
>>            <mailto:gmx-users-request@**gromacs.org<gmx-users-request at gromacs.org>
>> >
>>               <mailto:gmx-users-request at __gr**omacs.org<http://gromacs.org>
>>            <mailto:gmx-users-request@**gromacs.org<gmx-users-request at 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>
>> >
>>               <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>
>> >>
>>
>>
>>
>>        --         ==============================**__==========
>>
>>        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://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 at gromacs.org
>>        <mailto:gmx-users at 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-request at gromacs.org
>>        <mailto:gmx-users-request@**gromacs.org<gmx-users-request at 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>
>> >
>>
>>
>>
>>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110624/68e02ec0/attachment.html>


More information about the gromacs.org_gmx-users mailing list