From: Daniel Gaston (
Date: Tue Jun 30 2009 - 13:10:14 CDT

I'm not sure about most of your questions but in regards to your concern
about graphics clipping I would suspect that it is an issue with your
video card and OpenGL. I known on many of my systems I run into issues
like that with VMD (and other OpenGL programs) especially if the main
window is laying over some other open window. If I make sure no window
is behind it or overlapping with it the problem vanishes.


Steve Jensen wrote:
> Hi Everyone,
> I am using VMD for analyzing VASP POSCARS and I notice that there are
> certain things that I have to every time that I load a file or start a
> new session. I tried looking around for how to change these presets,
> but I was curious if any of you could help.
> Change default file type to POSCAR
> Change default view to orthographic
> Change default drawing method to VDW (w/ sphere resolution of say 14)
> Make it periodic in +x and +y
> Also, on another note, is there a way to specify my molecule as one
> unit so it could be easier to rotate/manipulate it or parts of it as a
> whole while leaving the surface alone? (group 10 atoms, leave the
> other 70 alone) Basically I am wondering if there is an easy way to
> try out different orientations of a molecule on a surface without
> having to apply tons of rotation and translation matricies in excel.
> Thank you so much for your help!
> Stephen
> PS- On a final note have people ever run into issues with clipping
> when running VMD on a cluster? I am on a redhat enterprise 4 x86 64
> bit cluster and when I load vmd all the graphics are constantly flashing.
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