[gmx-users] Re: Re: msd of com of bilayer

[David van der Spoel]

On Fri, 2004-03-19 at 06:52, Patel Ronak Y wrote:
> Dear Dr Spoel,
> 
> I used g_traj for calculation of com of bilayer.
> 
> For calculation of msd I used
> 
>     |r(t)-r(o)|^2
> msd=------------
>          4
>                       r(t)=coordinate at time t
>                       r(0)=coordinate at time 0
> 
> to calculate msd along x and y direction independently. The graph shows
> increasing and decreasing patterns instead of just increase that is
> expected.
It will increase on average (but not monotonically) if you take into
account the periodic boundary conditions (like what is done in g_msd).
However if you don't, it will just fluctuate.

For very long lipid simulations it is recommended to remove the 
c.o.m. motion for the bilayer.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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