[gmx-users] Free energy of transfer with accuracy

Eudes Fileti fileti at ufabc.edu.br
Tue Dec 9 18:41:25 CET 2008

Hi gmx-users,
I have tried to calculate the free energy of transfer of
a solute between two solvents by thermodynamic integration.
However, the dgdl plot I have obtained is not smooth enough to ensure
I have used a non homogeneous spacing for lambda. The first is from 0.0 to
0.4 (dl=0.04),
the second is from 0.405 to 0.48 (dl=0.005) and the third is from 0.48 to 1
Overall, I was performed 40 simulations.
As can be seen in the figure (
http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg ),
there is a large fluctuation in the region that goes from 0.40 to 0.48.
Each simulation was carried out by 0.5ns preceded by 0.15ns of
I am using soft-core whose parameters are:

; Free energy control stuff
free_energy              = yes
init_lambda              = 0.00
delta_lambda             = 0
sc_alpha                 = 1.3
sc-power                 = 1.0 (for this I also used 2).
sc-sigma                 = 0.47

In the example of the link sc-power=1, but I re-did the calculations with
and I found the same behavior (although the format of the plot was a little

Can you suggest me a way to calculate this free energy difference with
The perturbation free energy method could give better results?

Thank you
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170  Santo André - SP Brasil
skype: eefileti
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