[gmx-users] Bad calculated Free Energy values

[David]

On Fri, 2004-04-02 at 18:18, Ilya Chorny wrote:
> How many lambda values are you using?
>  
> Ilya
>  
>         -----Original Message-----
>         From: gmx-users-admin at gromacs.org
>         [mailto:gmx-users-admin at gromacs.org]On Behalf Of Alexandre
>         Suman de Araujo
>         Sent: Friday, April 02, 2004 3:26 AM
>         To: gmx-users
>         Subject: [gmx-users] Bad calculated Free Energy values
>         
>         
>         Hi GMX-ers!!!
>         
>         I´m performing some simulations to obtain free energy of
>         hydration of some ions (Ca+2, Sr+2 and Ba+2) using
>         oplsaa(tip3p for water) force field and the results aren´t so
>         good in my opinion. Look at the results below and the
>         experimental values (taken from book Burgess, Metal Ions in
>         Solution):
>         
>         DGh (kJ/mol)
>         
>         Ion           Calculated          Experimental       
>         Difference
>         
>         Ca+2         -1391                  -1591                    
>         200
>         Sr+2         -1248                  -1442                    
>         194
>         Ba+2         -1107                  -1317                    
>         210
>         
>         
>         Look that the difference between calc. and exp. values are
>         something about 200 kJ/mol, then I think this can be something
>         I´m not including in the calculations that results in error
>         with almost same values in three cases.
>         
You should first check numbers from other computations. Then you should
check which corrections should be made for Cut-off. These are
substantial. Check old papers by Straatsma and by Aqvist.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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