Sir, <br><br>I checked gmxdump -e ener.edr as suggested, I found that<br>there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5<br>when I calculated the average for these values using another<br>tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave <br>
some different answer as mentioned before in both 4.5.3 and<br>4.5.4 versions. Sorry I sent the mail twice as I did not receive<br>Dr. Mark's reply form the forum.<br><br>Thank you<br>With Regards<br>Kavya<br><br><br>
<br><div class="gmail_quote">On Wed, Aug 17, 2011 at 4:15 PM, Kavyashree M <span dir="ltr"><<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Sorry Sir, <br><br>I did not get that mail from the forum.<br><br>Thank you<br>With Regards<br>Kavya<div><div></div><div class="h5"><br><br><div class="gmail_quote">On Wed, Aug 17, 2011 at 12:11 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">This mail was answered already... Please pay attention.<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html</a><br>
<br>
Tsjerk<br>
<div><div></div><div><br>
On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com" target="_blank">hmkvsri@gmail.com</a>> wrote:<br>
> 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<br>
> confusion.<br>
><br>
> Thanking you<br>
> With Regards<br>
> M. Kavyashree<br>
><br>
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<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
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