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

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 19 08:56:01 CET 2004

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 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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