[gmx-users] Bad calculated Free Energy values
David
spoel at xray.bmc.uu.se
Fri Apr 2 19:17:01 CEST 2004
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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