<div class="gmail_quote">Dear users, <br><br>While calculating the box dimensions during a simulation<br>of 20ns I got some strange values of the averages -<br><br>Command used:<br>g_energy -f ener.edr -o box.xvg<br><br>Output:<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Box-X 0.00665539 1.4 0.219101 -4.28575 (nm)<br>Box-Y 0.00665606 1.4 0.219101 -4.28574 (nm)<br>
Box-Z 0.00470607 1 0.154928 -3.03048 (nm)<br><br>While the actual dimensions are 7.2, 7.2 and 5.1 respectively. I use<br>Gromacs-4.5.3, and 4.5.4 version also gave the same error. But <br>
when the .xvg file is examined it does not show much of the
error<br>indicated here. I also checked whether the is any discontinuity in <br>the .edr file using gmxcheck and there was data from 0 to 20ns <br>with no such discontinuity. I am attaching the corresponding .xvg plot. <br>
I had a similar problem before, and I was asked to check using <br>the new version. Which I did ad there was no difference. Meanwhile <br>I calculated the average values using other tools which gave 7.2, 7.2<br>and 5.1 respectively. So What is the problem here. Kindly clarify the confusion.<br>
<br>Thanking you<br>With Regards<br><font color="#888888"><font color="#888888">M. Kavyashree</font>
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