Re: infinite layer

From: Nicolas Belloy (
Date: Wed Apr 18 2007 - 06:06:52 CDT

Thanks a lot for the answer,
I think the most difficult part of the job is the creation of the patch ...

> 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.
> Peter
> 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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