[gmx-users] strange diffusion behaviour

[David]

On Thu, 2003-03-13 at 20:29, B. Nick wrote:
> 	
> 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?
Yes, if you have save velocities now and the in trr file you can use
g_traj.

Since you only have one molecule, your MSD will be noisy. The best you
can do is cut your trajectory in 10-20 bits and compute MSD's voor all
of these bits and the average.
> 
> Thanks for any help,
> Gitta
> 
> 
> 
> -- 
> Dr. Birgitta Nick
> DWI, Veltmanplatz 8, 52062 Aachen, Germany
> Tel. +49 241 4469138
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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