From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Feb 18 2012 - 10:57:01 CST

On Sat, Feb 18, 2012 at 10:45 AM, Philippe Bopp / temporary
<philippebopp_at_yahoo.com> wrote:
>
>  Hi
>
> question: What is quicksurf's philosophy with
> respect to periodic boundary conditions?
> It seems to me it draws periodic surfaces
> (if I select periodic) but does not compute
> the surface taking into account the periodicity.
>
> Am I right? Am I doing something wrong?

you are right and not doing something wrong.

most features in VMD and particularly graphical
representations do not consider periodic boundary
conditions. periodic display is achieved by simply
replicating the graphical objects. to have a real
periodic display, you currently have to replicate
the data (and hope to have enough RAM and
a fast GPU). check out "TopoTools::replicatemols":
http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-replicatemol-mol-nx-ny-nz-

> Does it depend (I could not find out how) on
> the order of the operations?

no. one has to keep in mind that VMD has its
roots in biomolecular modeling, primarily solvated
proteins where these issues are a minor concern.
over the years, VMD has come long ways to
improve the situation, but there is still a lot to do.

if you need better support for periodicity, you
may want to check out Tone Kokalj's XCrsyDen
http://www.xcrysden.org but that doesn't have
the VMD scripting magic and will bog down when
handling larger systems.

TANSTAAFL unfortunately.

salut,
    axel.

> thanks
>
> Philippe
>
>
>
>
>
> -----------------
> Philippe A. Bopp
>
> philippebopp AT yahoo.com       (private)
> Philippe.Bopp AT u-bordeaux1.fr (office)
> -----------------

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.