AMBER Archive (2007)

Subject: Re: AMBER: polarization and water density

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 13 2007 - 14:53:42 CDT

On Fri, Apr 13, 2007, Thérèse Malliavin wrote:
>
>
> My problem is that the density of water always increased up to around
> 1.1-1.15 and then the simulation stops, usually because of "vlimit
> exceeded for step".

It's not clear what the problem really is here. You are using a
non-polarizable water (TIP3P) with a polarizable protein, and it is possible
that the hydrogen atoms of the water are coming too close to some protein
atom. You might look for bad contacts in the final coordinates of one of the
failed runs

The only polarizable model I have a lot of experience with is ff02r1
(highly recommended in place of the original ff02) plus POL3 water. That
seems stable and doesn't give any obviously bad behavior. Others may wish to
comment on their experience using ff02 or ff02r1 with TIP3P. I think we used
to do things like that, but I haven't tried that for some time.

...regards...dac

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