[gmx-users] drift of simulation cell

[David van der Spoel]

Qing Zhu wrote:
> Hi All,
> 
> I am using gromacs to simulate a lipid/cholesterol mixed membrane. When 
> I looked at the trajectory using VMD, the whole simulation cell 
> laterally drifted very fast, and it looked like center of mass motion. 
> But when I set up the simulation, I did turn off the center of mass 
> motion. I don't know where this drifting motion came from, and it had 
> huge influence on the calculations of system diffusion property. So does 
> anyone know how to remove this kind of fast drifting motion from the 
> trajectory so that I can do some correct calculations on diffusion.
> 
you want to turn off center of mass motion for membrane and water 
separately. If you look closer you will probaböy see they move in 
opposite directions.

> Thanks
> 
> Qing Zhu
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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