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

Jose Borreguero 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
> 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120223/6997f960/attachment.html>

More information about the gromacs.org_gmx-users mailing list