[gmx-users] free energy of binding

Tao Li taol at rci.rutgers.edu
Tue Sep 20 18:31:41 CEST 2005

Hi, all, 

We would like to calculate the free energy of binding for two species in water with Gromacs. Basically the reaction of interest is like:  A + B --> complex, and we want the free energy of reaction (binding), delta G. 

We tried the LIE method first, but no good results have been yielded. We are thinking of using the FEP approach, but, we are not sure on how to perform such calculation.  Should I use a thermodynamic cycle like this: 

A (vacuo)  +  B (vacu0)  ---> Complex (vacu0)   delta_G1
 |                   |                          |
 |                   |                          |
A (Sol)    +    B  (Sol)    ----->  complex (solvent)   delta G

So, Delta G = Delta_G1 - Delta_solv(A) - Delta_solv(B) - Delta_solv(complex)

Can I get the free energy of binding directly without having to calculation all these solvation energies, and the gas phase binding energies? 

Thanks a lot for the help, 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050920/284f5364/attachment.html>

More information about the gromacs.org_gmx-users mailing list