[gmx-users] center of mass motion in lipid bilayer

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 11 22:13:28 CET 2007

Jian Dai wrote:
> Hello, everyone:
> I have a  system which is composed of a lipid bilayer and water layers 
> upon each monolayers.
> Now the problem is that after the simulation, the lipid bilayer shift 
> upward inside the simulation box , and makes the upper water layer 
> thinner, while the lower water layer thicker.
> In mdp file I turned off the COM for SOL and LIPID separately, and as a 
> default, comm_mode=angular.
> Do you have any idea?
> Thank you in advance.
> Jian
you shouldn't use angular with periodic boundary conditions, change it 
to linear.

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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