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

[David van der Spoel]

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.
________________________________________________________________________
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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