[gmx-users] strange diffusion behaviour

[B. Nick]

Dear all

I have a 10 ns trajectory of an 70 atom
organic molecule in water. I calculated
the diffusion coefficient using g_msd.
In the MSD plot I see a change in diffusivity
(increase) after about 2 ns MD time.

Can this be due to wrong COM motion removal?
I used no comm_grps parameter in my input file
(so it should be the whole system).
Or is this a result of wrong temperature
coupling, the tc_grps was set to SYSTEM.
Is there a simple way to calculate temperature of
solute and solvent separately from the trajectory?

Thanks for any help,
Gitta



-- 
Dr. Birgitta Nick
DWI, Veltmanplatz 8, 52062 Aachen, Germany
Tel. +49 241 4469138