<DIV> </DIV><DIV> </DIV><SPAN>On 16/08/11, <B class=name>Kavyashree M </B><hmkvsri@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAPLGqjrZR4m8us0-oE6XtiNN2pC7cpg3tHbbcjn9YL1qzQzsXw@mail.gmail.com type="cite">
<DIV class="mimepart text html">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. Kindly clarify the confusion.</DIV></BLOCKQUOTE>
<DIV> </DIV><DIV>That looks like a bug in g_energy. What does gmxdump -e ener.edr have to say about the BoX-?? values? </DIV><DIV> </DIV><DIV>Mark</DIV>