[gmx-users] Box-size

Kavyashree M hmkvsri at gmail.com
Tue Aug 16 12:06:23 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

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.

Thanking you
With Regards
M. Kavyashree
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110816/226f4302/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Box.png
Type: image/png
Size: 10170 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110816/226f4302/attachment.png>


More information about the gromacs.org_gmx-users mailing list