AMBER Archive (2004)

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

From: Chunhu Tan (tanc_at_uci.edu)
Date: Thu Nov 11 2004 - 19:53:58 CST

 Hi, All,

        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? 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?
       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?

Thanks in advance !

Chunhu
 

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