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

[Jose Borreguero]

Yes, the water certainly drifts along with the membrane. Umm, it is safe to
remove the COM momentum in an NPT (Langevin+piston) simulation?

Later I want to do a steered dynamics simulation for this system. The
external applied force will certainly produce a nonzero net momentum. Is it
safe to remove the COM momentum in this case?

-Jose


On Thu, Feb 23, 2012 at 8:35 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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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>
>
>
>
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