Re: AMBER: What does this error message mean?

From: Ioana Cozmuta <>
Date: Fri, 31 Oct 2003 07:46:46 -0800 (PST)


What temperature did you equilibrate your system? If it is room
temperature and you add cold molecules (initial velocities zero) to that
you favor large fluctuations, the transition of your new molecules to the
equilibrium temperature is not smooth enough.
You are also saying that you had water previously in the system but it is
not clear if you reset velocities to zero to all the water molecules
(equilibrated + new ones)?
Anyhow, I think you should take a step back and heat up the system slowly
whenever you add something new to it. At least you could define
a random initialization of velocities to the equilibrium temperature
(whatever value that is) and reequilibrate the water around your system.

Hope this helps,

On Fri, 31 Oct 2003, nie beining wrote:

> Dear Amber users,
> I added a tiny water box to an equilibrated system including a
> protein, ions and water molecules (14000 atoms). There are about
> 50-70 water molecules in the box and I set the velocities of these
> water molecules to zero. Then I started running MD simulation using
> the velocities of equilibrated system and of additional water
> molecules with sander. Sander gave me the following error message
> NITER, NIT, LL, I AND J ARE : 0 1 686 1427 1428"
> in the beginning and quit computing. Could you please tell me what this
> message means? How can I solve this problem? Thanks a lot!
> Beining
> ---------------------------------
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Received on Fri Oct 31 2003 - 15:53:01 PST
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