Date: Thu Jun 08 2006 - 12:13:31 CDT
After searching the old posters on namd-list, I still cannot get complete
answer for my FEP problem. Please share some opinion.
My system includes a cofactor A change to B (total charge change of 2) and
two counter-ions Cl change to water molecules (to neutralize the system).
I did add some constraint to the position of those two Cl ions and water
molecules. Now it seems that my FEP simulation in NAMD did work. I have
checked the trajectory of the simulation, and didn't see anything wierd.
However, the accumulated net free energy change is huge during the
simulation (about 300 from the fepout file). I suspect this may come from
the solvation energy of the ions (Cl to water). How much energy
contributed from the solvation should I expect? And how can I better
estimate the energy change just for the cofactor A to B?
Should I mutate the Cl ion to a dummy atom instead? Is my problem related
to the end-VDW clashes?
Thanks a lot!
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