[gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?
Mark.Abraham at anu.edu.au
Thu Feb 23 14:35:03 CET 2012
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.
> 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
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