On 17/08/2011 9:13 PM, Kavyashree M wrote:
Sir,
I checked gmxdump -e ener.edr as suggested, I found that
there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5
when I calculated the average for these values using another
tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave
some different answer as mentioned before in both 4.5.3 and
4.5.4 versions. Sorry I sent the mail twice as I did not receive
Dr. Mark's reply form the forum.
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.
Mark
Thank you
With Regards
Kavya
On Wed, Aug 17, 2011 at 4:15 PM, Kavyashree M <hmkv...@gmail.com
<mailto:hmkv...@gmail.com>> wrote:
Sorry Sir,
I did not get that mail from the forum.
Thank you
With Regards
Kavya
On Wed, Aug 17, 2011 at 12:11 PM, Tsjerk Wassenaar
<tsje...@gmail.com <mailto:tsje...@gmail.com>> wrote:
This mail was answered already... Please pay attention.
http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html
Tsjerk
On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M
<hmkv...@gmail.com <mailto:hmkv...@gmail.com>> wrote:
> 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. Which I did ad there was no difference.
Meanwhile
> I calculated the average values using other tools which gave
7.2, 7.2
> and 5.1 respectively. So What is the problem here. Kindly
clarify the
> confusion.
>
> Thanking you
> With Regards
> M. Kavyashree
>
> --
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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