[gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?
borreguero at gmail.com
Thu Feb 23 12:27:13 CET 2012
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
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
> 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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