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

[Kavyashree M]

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.

Thank you fro answering.

With Regards
M. Kavyashree


On Fri, Jun 24, 2011 at 4:57 PM, Justin A. Lemkul <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>> 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 | (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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