Re: infinite layer

From: Peter Freddolino (
Date: Fri Apr 13 2007 - 21:57:58 CDT

Hi Nicolas,
you should be able to do this so long as you make one set of strands,
and then properly align the strands at each end of the box to line up
with each other and set periodic boundary conditions with the dimensions
of your strands (you can try different box sizes in VMD by showing
periodic images in the periodic tab of graphical representations and .
You'll need to make a patch to form a peptide bond between the
appropriate residues at the end of strands to connect them across the
boundary conditions; you can use the DISU patch as a template for this,
and apply it to residues that are adjacent to each other across the
boundary conditions.

While the steps above will let you set up the technical aspects of such
a simulation, though, you need to be very careful about exactly what
you're doing. Obviously, this won't really give you an "infinite" beta
sheet; and if you simulate for too long, or apply some sort of
significant pulling to the system, for example, you're going to run into
finite size effects.


Nicolas Belloy wrote:
> Dear Namd users,
> I'd like to simulate an infinite layer of beta-strands in the x, y
> directions.
> How can I do this with NAMD using PBC ? Is it also possible to create
> a covalent bond between the beginning of a strand and the end of its
> image over PBC?
> Thanks
> Nicolas
> ---------------------------------------------------------
> Nicolas Belloy (PhD student)
> Unité CNRS 6198 - UFR Sciences Exactes et Naturelles
> Moulin de la Housse -51687 Reims Cedex 2
> ---------------------------------------------------------

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