question about FEP calculation

Date: Wed Mar 01 2006 - 11:11:37 CST

Deal all,

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 (2 charges difference). 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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