AMBER Archive (2009)

Subject: Re: [AMBER] Water-molecules

From: case (case_at_biomaps.rutgers.edu)
Date: Sun Apr 26 2009 - 17:35:36 CDT

On Sun, Apr 26, 2009, sikander azam wrote:
>
> I m working to simulate water molecules and successfully minimized the
> system along with heating.

You appear to be running a non-periodic simulation, that contains(?) "water
molecules". It is likely that some of the molecules are moving far away from
the rest. You should visually look at your system, and see what is happening.

If the system is indeed set up the way you want it to be, you could (a) follow
the instructions in the error message; (b) run such a system with igb=6
(assuming you are not using "extra points"). But most often, this error
occurs when the systems is not doing what it should. But only you can tell
that.

...dac

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