[gmx-users] Box-size: please reply

[Kavyashree M]

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>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> 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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