[gmx-users] Free energy

[chris.neale at utoronto.ca]

In addition to Justin's comments, check your convergence with block  
averaging. Is there a systematic energy drift as you increase the  
amount of sampling prior to each block? Also, try applying your method  
to Na+ and Cl- in a box of water. If you can't get that free energy  
correctly, then you certainly cannot get the free energy you are  
looking at given the method and amount of sampling. Finally, check on  
your ions. You've got a lot of them, so chances are that they exist  
near the binding site in some of your simulations. Have you converged  
the ion distribution? This can be harder than you expect.

Chris.

-- original message --

Dear All
I estimated protein-ligand free energy about -300 kj

Is it logical?I think it is wrong.what do you think?
what is the range of correct value for a typical protein-ligand?
protein=660 residue
ligand=25 atom
water=4670
Na=118
Cl=120

thanks in advance
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