AMBER Archive (2009)

Subject: Re: [AMBER] NAB md function prints strange output

From: David A. Case (
Date: Mon Feb 09 2009 - 06:58:43 CST

On Mon, Feb 09, 2009, Jochen Heil wrote:

> For some reason, i get "nan" for the
> total energy as well as the nonpolar part. Since i switched off GBSA, i
> would expect zero, but "nan" seems to point to a wrong setup or logical
> error, especially when printed in the total energy column.

I haven't ever seen anything like this. The nan for "total" just arises
because it is the sum of the other components. And, since MD depends
only on the forces (not the total energy), and the forces look OK, it's
possible that the trajectory is OK as well. But this should be tracked looks like a bad initialization or memory overwrite(?).

What happens if you add a call to mme() after a (short) MD run? You
might want to try a debugger or post a small example that allows the
problem to be reproduced.


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