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

[Mark Abraham]

On 23/02/2012 10:27 PM, Jose Borreguero wrote:
> I am not referring to any drift of the whole system, but to the 
> diffusion of the lipid bilayer only. Diffusion of molecules in water 
> is to be expected given sufficient time. I wonder what is a reasonable 
> restraint to keep the center of mass of the membrane at Z=0.0

You can't have the bilayer drift unless the water drifts with it or 
through it. The former is more likely, thus you likely have COM motion.

Mark

>
> -Jose
>
> On Wed, Feb 22, 2012 at 9:04 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     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
>
>     Mark
>
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