[gmx-users] Box-size: please reply

[Mark Abraham]

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 <hmkvsri at gmail.com 
> <mailto:hmkvsri at 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
>     <tsjerkw at gmail.com <mailto:tsjerkw at 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
>         <hmkvsri at gmail.com <mailto:hmkvsri at 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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