VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 25 2006 - 13:51:41 CDT

Hi,
  VMD should have no trouble reading the trajectory or the unit cell
information from the AMBER trajectory, regardless of the space filling
unit cell shape represented. The challenge is to interpret the unit cell
side lengths and angles in the AMBER trajectory correctly when doing things
like coordinate wrapping/unwrapping, and so on with your own scripts.
The PBC display features in VMD currently work for the simpler box
shaped unit cells, but you won't be able to display a full truncated
octahedron unit cell conveniently with the built-in interfaces at present.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 25, 2006 at 01:05:06PM -0500, Kenley Barrett wrote:
> Dear VMD community,
>
> I am going to be running some molecular dynamics simulations in AMBER, and I
> want to analyze the resulting trajectory files in VMD. AMBER allows a choice
> of a periodic box or a periodic truncated octahedron. The AMBER manual
> recommends using the truncated octahedron. Will VMD understand this kind of
> periodicity? Would I still use "crdbox" as the file type for the trajectory
> file?
>
> Thank you very much for any advice.
>
> Kenley 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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