Date: Wed Mar 01 2006 - 11:11:37 CST
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!
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:20 CST