From: John Stone (
Date: Mon May 15 2006 - 12:39:30 CDT

  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:

  John Stone

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

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