AMBER Archive (2005)

Subject: Re: AMBER: Message in .out file

From: David A. Case (case_at_scripps.edu)
Date: Wed May 18 2005 - 01:38:40 CDT

On Tue, May 17, 2005, Atilio Anzellotti wrote:
>
> I am running a dynamics with DNA in WATBOX216 and I found
> out that in some points of my .out file the message below
> can be seen:
>
> check COM velocity, temp: 0.003173 0.02(Removed)
>
> I am particularly worried about the "removed" part, is this
> normal?

Yes; sander will remove center-of-mass motion every nscm steps (1000 by
default). Set nscm=0 to turn this behavior off, but what you see above is
quite normal. It says that the temperature corresponding to COM motion
is 0.02 K, which is really very small.

....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu