AMBER Archive (2007)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Dec 18 2007 - 20:26:34 CST

Okay, Yong and I discussed this in a bit more detail. It indeed seems
possible to me to construct a tool that would allow you to do this, but the
current rub is that ptraj doesn't handle it. SO the basic assertion that
you should not do diffusion analysis of a trajectory that has been wrapped
remains, though you COULD in theory do it with the code that reconstructs
absolute trajectories for the atom set.
Regards - Bob
----- Original Message -----
From: "Yong Duan" <duan_at_ucdavis.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, December 18, 2007 12:47 PM
Subject: RE: AMBER: pmemd: same rst, different result?

>
>> .... 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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