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On 17/08/2011 9:13 PM, Kavyashree M wrote:
<blockquote
cite="mid:CAPLGqjpJ=Da-9K_J73tA+Nf0hgdntQ=OQDQbAzLSdWWtb_b8Gg@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
OK, that looks like a bug of some kind. Please file an issue at
redmine.gromacs.org (the server is down at the moment) uploading
your input and output files and I'll take a look at it. Thanks.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPLGqjpJ=Da-9K_J73tA+Nf0hgdntQ=OQDQbAzLSdWWtb_b8Gg@mail.gmail.com"
type="cite"><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 moz-do-not-send="true"
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 class="h5"><br>
<br>
<div class="gmail_quote">On Wed, Aug 17, 2011 at 12:11 PM,
Tsjerk Wassenaar <span dir="ltr"><<a
moz-do-not-send="true"
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 moz-do-not-send="true"
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><br>
On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M <<a
moz-do-not-send="true"
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>
</div>
</div>
> --<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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