> .... do a run with iwrap 1 to get coordinate wrapping,
> but note that you lose some trajectory info at this point - ie., you can't
> calculate diffusion through this operation
This sounds like another urban myth :).
I think you can calculate the diffusion, assuming you save frames often
enough and your system is not ridiculously small. You may even be able to
recover the "unwrapped" coordinates if a strict wrapping is done (i.e.,
without shifting the COM) by reversing the PBC to X(t+dt)-X(t).
yong
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Dec 19 2007 - 06:07:31 PST
