VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 15 2006 - 12:39:30 CDT

Michel,
  Did you try unwrapping the trajectory before doing your analysis?
It sounds like for this case, working with an unwrapped trajectory would
be much easier. Have a look at Jan's pbcwrap script, you could probably
adapt it to unwrap as well:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcwrap/

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 12, 2006 at 09:40:59AM +0200, L. Michel Espinoza-Fonseca wrote:
> Hi there,
>
> I'm trying to analyze a trajectory of a complex between a big protein
> and a peptide. The problem is that, when I look at some parts of the
> simulation, the two parts of my system "split": the peptide is moving
> to the other side of the cell --which is normal, I'm using PBC--,
> while the big protein does not. The thing is that I need the complex
> to stay together for the analysis -RMSD, RGYR, etc-. I've miserably
> tried to put everything together, but I got nothing. Do you have any
> suggestions on how to achieve this?
>
> Thank you!
>
> Cheers,
> Michel 

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