[gmx-users] charge changes in free energy calculations

friendli friendli2000 at gmail.com
Fri Sep 26 09:14:30 CEST 2008

Dear all,

I have a mutation free energy calculation from D(asp) to E(glu). The 
charge is not changed for the overall mutation. However, following Dr. 
David Molbey's suggesion, electrostatic and VDW interaction should be 
modified separately, so in the first step we need to turn off the charge 
from D(-1) to D(0).

I learn from the mailing list that it is problematic to do FE 
calculations with different charges for initial and final states.
So is that safe to turn off the charge for D and turn on the same charge 
for E in this case?
If not, it that OK to perform mutation FE calculation in one step?
or there is no safe way to handle this kind mutations, i.e. mutating 
charge groups, currently without special correction?

thank a lot


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