Re: membrane constraints on thickness

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Fri Jan 26 2007 - 07:27:21 CST

Perhaps my question is not clear.

I want to do the following in the same simulation:

- Constrain lipids in the z-direction
- Constrain the protein about its mean position

Can this be done in the same script using the selectConstraints command ?
Or will both the protein and lipids be constrained in the z-direction ?

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
-----------------------------

On Fri, 26 Jan 2007, Peter Freddolino wrote:

> Hi Himanshu,
> you can have different values in the B column of all atom -- those with
> a 0.00 in that column will not be constrained.
> Peter
>
> Himanshu Khandelia wrote:
> > 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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