[gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 23 03:04:07 CET 2012

On 23/02/2012 10:26 AM, Jose Borreguero wrote:
> Dear GROMACS users,
> While simulating a DLPC membrane, I noticed that it tends to diffuse 
> along the normal (Z-axis) component. Is there a 'standard' restrain 
> that is used to prevent such diffusion?
> The first option I thought was to restrain the  center of mass of the 
> whole membrane along the Z-axis, but I don't know what is a reasonable 
> value for the force constant.
> If anyone has any experience dealing with this kind of problem, please 
> do reply.

Diffusion of the center of mass of the whole system is something that 
can be removed by an existing mechanism. See manual 7.3.3

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