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 <darre...@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 > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php