## Bug #194

### shape of g_msd graph depends on time interval evaluated

**Description**

Hi,

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,

Gregor Bruns

### History

#### #1 Updated by Gregor Bruns over 12 years ago

Created an attachment (id=277)

Collection of msd graphs showing the problem.

#### #2 Updated by Gregor Bruns over 12 years ago

Created an attachment (id=278)

.mdp file used in the simulation

#### #3 Updated by David van der Spoel over 12 years ago

Could you please specify the command line you used? In particular you may want to specify -trestart to be 0, and for comparing diffusion coefficients you also should check the-beginfit and -endfit options.

#### #4 Updated by David van der Spoel over 12 years ago

Did my previous comments resolve the problem?

#### #5 Updated by Berk Hess about 12 years ago

Hi,

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.

Berk.