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
<<attachment: Box.png>>
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