Re: AMBER: Explicit water opinion

From: David Cerutti <>
Date: Fri, 13 Apr 2007 15:58:32 -0700 (PDT)

The TIP3P water is "weak" in the sense that it doesn't get some features
of the liquid correct, even at ambient temperature where it's supposed to
work (the second peak in the O-O RDF and the diffusion coefficient, for
example). But, another problem with using TIP3P in modern simulations is
that it's not designed to work with long-range electrostatics, rather a
sort of cutoff (rarely used anymore) based on O-O distance.

SPC/E, on the other hand, which is what you get when you specify an SPC
box, is designed to work with long-range electrostatics and Lennard-Jones
tail corrections which AMBER uses by default. It is probably the best
three-site rigid point-charge model available--all sorts of thermodynamic
properties are reproduced correctly at ambient conditions, and even the
VLE looks better (although that's pushing it).

There is a reparameterization of TIP3P by Charlie Brooks's group that
makes it compatible with long-range electrostatics (and the cutoff they
used to fit it was so large that, if you want to use a small cutoff like
8A, the default long-range dispersion correction will also work nicely
with that model). I think that the stuff they produced was roughly as
good as SPC/E, but to use their version of TIP3P will take you some more

For more information, go to:

But, I'd just use the SPC box.


On Fri, 13 Apr 2007, Hayden Eastwood wrote:

> Dear Amber Users
> I am about to attempt an explicit water simulation on a protein (40 amino
> acids) bonded to a sacharide partner. I am wondering which explicit model is
> best, many papers have published findings with SPC and TIP3P boxes. However,
> I've recently been to a conference in which many people derided TIP3P as
> being weak. Is there any agreement as to which water representation is most
> accurate? (Or at least most appropriate for a small protein with a charge of
> approx. +6).
> Many thanks
> Hayden Eastwood
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Received on Sun Apr 15 2007 - 06:07:46 PDT
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