[gmx-users] Box-size: please reply

[Tsjerk Wassenaar]

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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> 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