[gmx-users] Box-size: please reply

Kavyashree M hmkvsri at gmail.com
Wed Aug 17 08:12:32 CEST 2011

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

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. Which I did ad there was no difference. Meanwhile
I calculated the average values using other tools which gave 7.2, 7.2
and 5.1 respectively. So What is the problem here. Kindly clarify the

Thanking you
With Regards
M. Kavyashree
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