From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jan 26 2007 - 07:01:35 CST
you can have different values in the B column of all atom -- those with
a 0.00 in that column will not be constrained.
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
> 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 ?
> 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.
>> Himanshu Khandelia wrote:
>>> 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 Khandelia
>>> Research Assistant Professor (Postdoc)
>>> MEMPHYS, Center for Membrane Physics
>>> University of Southern Denmark (SDU)
>>> Odense M 5230, Denmark
>>> Phone: +4565503510
>>> email: hkhandel_at_memphys.sdu.dk
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