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 <[email protected]
<mailto:[email protected]>> 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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