[gmx-users] Unexpected behavior of g_msd

Darrell Koskinen darrellk at ece.ubc.ca
Wed Nov 25 07:42:36 CET 2009

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?



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