[gmx-users] Box-size

[Mark Abraham]

On 16/08/11, Kavyashree M <hmkvsri at gmail.com> wrote:

> 
> Dear users, 
> 
> While calculating the box dimensions during a simulation
> of 20ns I got some strange values of the averages -
> 
> Command used:
> g_energy -f ener.edr -o box.xvg
> 
> Output:
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Box-X                    0.00665539        1.4   0.219101   -4.28575  (nm)
> Box-Y                    0.00665606        1.4   0.219101   -4.28574  (nm)
> Box-Z                    0.00470607          1   0.154928   -3.03048  (nm)
> 
> While the actual dimensions are 7.2, 7.2 and 5.1 respectively. I use
> Gromacs-4.5.3, and 4.5.4 version also gave the same error. But 
> when the .xvg file is examined it does not show much of the  error
> indicated here. I also checked whether the is any discontinuity in 
> the .edr file using gmxcheck and there was data from 0 to 20ns 
> with no such discontinuity. I am attaching the corresponding .xvg plot. 
> I had a similar  problem before, and I was asked to check using 
> the new version. Kindly clarify the confusion.
> 

 
That looks like a bug in g_energy. What does gmxdump -e ener.edr have to say about the BoX-?? values? 
 
Mark
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