Re: AMBER: separate solvent-solvent and solvent-solute interaction

From: David A. Case <>
Date: Mon, 21 Feb 2005 09:07:24 -0800

On Mon, Feb 21, 2005, Ye MEI wrote:
> How to separate solvent-solvent and solvent-solute interaction energy from
> total interation during MD simulation with sander?

First: note that the two most common simulation protocols (explicit solvent
with PME and implicit solvent with PB or GB) are not pair-wise decomposable
force fields. In these cases, there is no clean separation between
solvent-solvent and solvent-solute interactions. So you need to ask yourself
if this is what you really want, and think hard about what your definition of
these terms is (which will depend on how you are going to use the results.)

Second: you can define the solute as a perturbation, so that in the lambda=0
state you have the real system, and in lambda=1 you have removed *just* those
parts of the force field that you have identified as solute-solvent
interactions, keeping all other solute-solute interactions unchanged. The
if you set icfe=1 and run at lambda=0, you would get at each step the
solute-solvent interaction energy (as implicitly defined by the way you set
up the perturbation.) You should figure on having to play with this for a
while to make sure that you are getting what you really want.

Note that sander internally has no conception of what is the "solute" and what
is the "solvent". You would have to use a trick like that above to generate
such a distinction.

.....hope this helps....dac

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Received on Mon Feb 21 2005 - 17:53:02 PST
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