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<DIV><FONT face=Arial size=2>Hi, all, </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>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. </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>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: </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>A (vacuo) + B (vacu0) --->
Complex (vacu0) delta_G1</FONT></DIV>
<DIV><FONT face=Arial
size=2> |
|
|</FONT></DIV>
<DIV><FONT face=Arial
size=2> |
| |</FONT></DIV>
<DIV><FONT face=Arial size=2>A (Sol) +
B (Sol) -----> complex
(solvent) delta G</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>So, Delta G = Delta_G1 - Delta_solv(A) -
Delta_solv(B) - Delta_solv(complex)</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Can I get the free energy of binding directly
without having to calculation all these solvation energies, and the gas phase
binding energies? </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks a lot for the help, </FONT></DIV>
<DIV><FONT face=Arial size=2>Terri</FONT></DIV></BODY></HTML>