question about total charge change in FEP calculation

Date: Thu Mar 02 2006 - 10:01:23 CST

Anyone has some experience with FEP and total charge change during the
simulation, please give me some advice and share some experience.

I would like to perform a free energy perturbation calculation in NAMD.
It's a simple mutation to the cofactor of the protein. However, the total
charge of the protein+cofactor system changed (from 6+ to 4+). So the
beginning and ending structures would have different number of
counter-ions. How should I handle such charge change in FEP calculation?

Thanks a lot!

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