Re: membrane constraints on thickness

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Fri Jan 26 2007 - 03:45:40 CST

Thanks Peter. SelectConstraints should work, except that I would want some
of the atoms of the system constrained along the z-coordinate, and the
rest of the atoms just to be constrained harmonically about their mean
position.

If I use a pdb file with the force constant values in the B column, would
not all the atoms be constrained along the z-direction when using
selectconstraints ? If so, is there another way out ?

-Himanshu

On Thu, 25 Jan 2007, Peter Freddolino wrote:

> 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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