Re: AMBER: Solvation free energy of a charged molecule.

From: Chunhu Tan <tanc.uci.edu>
Date: Fri, 12 Nov 2004 10:43:32 -0800

Dear Dr. Case,

      I am sorry I have made a wrong statement, what I want to calculate is
the electrostatic contributions of solvation free energy, the first step you
mentioned.
      Thanks again for your response!

Regards,
Chunhu
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
To: <amber.scripps.edu>
Sent: Friday, November 12, 2004 8:11 AM
Subject: Re: AMBER: Solvation free energy of a charged molecule.


> On Thu, Nov 11, 2004, Chunhu Tan wrote:
>>
>> I want to know, if I can use the Sander TI to calculate the
>> solvation free energy of a CHARGED molecule. For example, I performed
>> Sander TI for an ARG analog ( +1 charged) in a water box and in gas
>> phase,
>> the integration of DV/DL of these two process are 130.4(gas) and
>> 180.5(water), so, if the difference (-50.1) is the solvation free energy
>> of
>> this molecue?
>
> It's not clear what "process" you were simulating, that is, what the
> lambda=0
> and lambda=1 end states were for your two calculations. To get the total
> solvation free energy, you would need to convert your model compound to
> nothing in both the gas phase and in solvent, and then take the
> difference.
> This would probably be done in two steps, one in which you remove all of
> the
> charges, and a second in which you convert all atoms to dummy atoms.
>
> As I know, when the system has nonzero net charge, uniform
>> neutralizing plasma will be added implicitly in order to perform the PME,
>> my question is, if this have any effect on the solvation free energy? If
>> yes, how I can find it out?
>
> For reasonable size boxes, the effects are very small; see, e.g.
>
> %A T. Darden
> %A D. Pearlman
> %A L.G. Pedersen
> %T Ionic charging free energies: Spherical versus periodic boundary
> conditions
> %J J. Chem. Phys.
> %V 109
> %P 10921-10935
> %D 1998
>
>> By the way, in his J. Chem. Phys. 2003 paper, Dr. Darden said that
>> "ischarged" option in Sander was used, but I can not find this word in
>> the
>> manual (7 and 8), is this defaulted?
>
> yes.
>
> ...dac
>
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Received on Fri Nov 12 2004 - 18:53:01 PST
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