Re: membrane constraints on thickness

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jan 25 2007 - 13:24:21 CST

You may want to have a look at the selectConstraints feature documented
at http://www.ks.uiuc.edu/Research/namd/2.6/ug/node28.html, which allow
you to constrain atoms only along certain axes.
Peter

Himanshu Khandelia wrote:
> Hello,
>
> I am equilibrating a protein in a membrane. The simulation box initially
> has a larger area than the calculated area based on area per lipid, and
> the cross sectional area of the protein.
>
> In order to equilibrate it to the right area, I need to restrict the
> thickness of the bilayer, while allowing the area to reduce gradually
> under (preferably) NPT circumstances. Is there a harmonic potential in
> NAMD that can be enforce upon the headgroups to keep their average
> z-coordinate fixed ?
>
>
> Thank you
>
> -Himanshu
>
> ----------------------------
> Himanshu Khandelia
> Research Assistant Professor (Postdoc)
> MEMPHYS, Center for Membrane Physics
> University of Southern Denmark (SDU)
> Odense M 5230, Denmark
> www.memphys.sdu.dk
> Phone: +4565503510
> email: hkhandel_at_memphys.sdu.dk
> -----------------------------
>
>

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