[gmx-users] Unexpected behavior of g_msd

[Tsjerk Wassenaar]

Hi Darrell,

You can check whether the output is identical to a trajectory of the
specified frames...
It may well be that the counting for the regression is done on  the frames read:
100 - 60 = 40 ps
Then 4 and 35.9 would correspond to 64 and 95.9. The answer is in the
code... But using a subtrajectory may give you good hint.

Hope it helps,

Tsjerk

On Wed, Nov 25, 2009 at 7:42 AM, Darrell Koskinen <darrellk at ece.ubc.ca> wrote:
> Dear GROMACS-ites,
> I am a little confused by the behavior of g_msd. I have a trr file with data
> points from t=0 to t=100 ps and thought that the following command would
> perform a regression for the data points between t=60 ps and t=100 ps to
> determine the diffision constant of the ammonia gas in the simualtion:
>
> *g_msd -f mdtraj.trr -s mdtopol.tpr -type x -b 60 -e 100*
>
> However, the output:
> *
> /trn version: GMX_trn_file (single precision)
> Reading frame     900 time   90.000
>
> Used 4 restart points spaced 10 ps over 39.9 ps
>
> Fitting from 4 to 35.9 ps
>
> D[       NH3] 3625.5647 (+/- 2802.0500) 1e-5 cm^2/s
> /*
> seems to indicate that the regression was performed between t=4 ps and
> t=35.9 ps.
>
> Could you please explain to me what is happening?
>
> Thanks.
>
> Darrell
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist