shape of g_msd graph depends on time interval evaluated
the shape of the g_msd .xvg graph seems to depend on the last frame evaluated (-e option).
I ran a 2 ns simulation of 486 ion pairs of 1,3-dimethylimidazolium chloride and evaluated the mean square displacement with g_msd. One would expect that the shape of the graph does not differ between 0 ps and 1000 ps if one evaluated the trajectory first between 0 and 2000 ps and then between 0 and 1200 ps (using the same input data file of course). Instead I got the contrary result, an increasing slope at the end of the graph, regardless of the last evaluation frame specified.
In the attachment msd-comparison.xvg I have collected four graphs created by g_msd with the same input trajectory, each beginning at 0 ps and ending at a different time, the problem is obvious.
This problem did occur in other simulations I ran, but in some other simulations the data analysis worked quite well (with minor discrepancies in slope).
My gromacs package was built 2008-17-03 on gentoo Linux.
Thanks for helping,
#5 Updated by Berk Hess about 12 years ago
I think you did not understand correctly what is in the graph.
The time t in the graph is not the actual simulation time,
but the time period over which the displacement is determined.
This is done for many different starting points (option -trestart),
not only starting at trajectory frame time 0.