Re: AMBER: shake

From: Carlos Simmerling <>
Date: Fri, 19 Aug 2005 12:45:16 -0400

you would have to change to code to do this-- probably not difficult to
change a pointer, but in my opinion the Amber force fields are not really
designed to give proper dynamics for bonds involving hydrogen. In fact
one of the reasons to constrain them is that they really are not described
well by classical potentials. You might be better using a force field with
a functional form that is designed to reproduce bond dynamics. For
the most part Amber is not.

Gustavo Pierdominici Sottile wrote:

> Dear list,
> I want to run a dynamic with explicit solvent (tip3p model).
> In the DNA tutorial, it is mentioned that when using such a water
> model it is essential that the hydrogen atom motion of the water also
> be fixed since failure to do this can lead to very large inaccuracies
> in the calculation of the densities,etc. I can not use SHAKE because
> the dynamics of an hydrogen atom is what I want to see. Is the any way
> to constrain only the hydrogen atoms of water molecules?. If this is
> not possible, is it possible to leave SHAKE off, using tip3p?
> Thanking in advance
> Gustavo

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Received on Fri Aug 19 2005 - 17:53:00 PDT
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