[gmx-users] Box-size: please reply

[Kavyashree M]

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.

Thank you
With Regards
Kavya



On Wed, Aug 17, 2011 at 4:15 PM, Kavyashree M <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>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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