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

Kavyashree M hmkvsri at gmail.com
Fri Jun 24 14:55:44 CEST 2011 

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.

Thank you
With Regards
M. Kavyashree

On Fri, Jun 24, 2011 at 5:53 PM, Kavyashree M <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> 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>> 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>>> 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> | (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 | (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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