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

From: Ye MEI <>
Date: Tue, 22 Feb 2005 11:21:48 +0800

Dear David,

Thank you very much for your reply.
We are developing methods to calculate the solvation free energy of
macromolecules based on quantum mechanics.
But we cannot think out a way to calculate the cavitation energy of solvent
also based on quantum mechanics at present. So we have to rely on molecular
mechanics. My difficulty now is the energy difference of water box with and
without a cavity accommodating a solute molecule.
I am sorry that I use the nomenclature from quantum mechanics such as solute,
solvent and cavity.
I highly appreciate your suggestions to achieve this.
Thank you in advance and best regards.


======= 2005-02-22 01:07:24 David A. Case wrote =======

>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
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Feb 22 2005 - 03:53:00 PST
Custom Search