[gmx-users] Bad calculated Free Energy values

[David]

On Fri, 2004-04-02 at 17:28, Alexandre Suman de Araujo wrote:
> David wrote:
> > 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.
> > 
> >   
> Thank´s David. I´ve read Aqvist paper but not Straatsma... I´ll search
> for it. But isn´t there any paper that report free energy calculations
> made by GROMACS?? I didn´t find anyone.
> Thank´s.
yes, but not for ions


A. Villa and A. E. Mark Calculation of the free energy of solvation for
neutral analogues of amino acid side chains.
J. Comput. Chem, 23 (2002) 548-553.


> 
> -- 
> Alexandre Suman de Araujo
> asaraujo at if.sc.usp.br
> UIN: 6194055
> IFSC - USP - São Carlos - Brasil
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-- 
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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