Re: infinite layer

From: Peter Freddolino (
Date: Tue May 01 2007 - 11:17:28 CDT

Hi Nicholas,
this is actually just a visual artifact in VMD. Whenever you do a
simulation in NAMD, the bond between two atoms will be taken to be
whichever distance is closer between the atoms in the same cell and
those in periodic images. This almost always just means taking the bond
for the same cell, but in your case it will lead to the correct result.
We're still working on beefing up VMD's understanding of periodic
boundary conditions, though, so it should display correctly in the
future. You should verify that the ends do indeed line up by viewing the
periodic cells in VMD, but don't worry if that bond isn't displayed

Nicolas Belloy wrote:
> Hi,
> I've created the strands with the NONE option for the terminii (well
> aligned in the x direction). The "a" size of the cell let around 1.6A
> between the Nter and Cter atoms in PBC.
> I try to create a bond between each strand and their images in PBC.
> I've found a patch called LINK in the Charmm topology file.
> PRES LINK 0.00 ! linkage for IMAGES or for joining
> segments ! 1 refers to previous (N
> terminal) ! 2 refers to next (C
> terminal) ! use in a patch
> statement BOND 1C
> 2N
> ANGLE 1C 2N 2CA 1CA 1C
> 2N ANGLE 1O 1C 2N
> 1C 2N 2HN DIHE 1C
> 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
> DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C
> 2N DIHE 1CA 1C 2N 2HN 1CA 1C 2N
> 2CA DIHE 1O 1C 2N 2HN 1O
> 1C 2N 2CA IMPR 2N 1C 2CA 2HN
> 1C 1CA 2N 1O IC 1N 1CA
> 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N
> 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC
> 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000
> 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000
> 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000
> 180.0000 0.0000 0.0000
> It works fine but create a bond between the extremities of the strands
> themselves not with their images. Is this patch a good idea ? Maybe
> I've just forgotten a keyword to orient the bond in the +x/-x
> direction ... or it's just a visual artefact of VMD.
> Thanks
> Nicolas
> 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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