AMBER Archive (2007)

Subject: RE: AMBER: pmemd: same rst, different result?

From: Yong Duan (duan_at_ucdavis.edu)
Date: Tue Dec 18 2007 - 11:47:31 CST

> .... 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

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