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

[Justin A. Lemkul]

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://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

========================================