dear all
I want to calculate the free energy change in converting one small
molecule (A) to another (B) in solution using TI approach by pmemd.
But I am not sure whether the change of internal energies (such as bond,
angle, and dihedral energies) are included in the besides VDW and
electrostatic energies, because molecule A and B has different number of
atoms.
Could you please give me some guidance? Thanks a lot.
Meiting,
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Received on Mon Dec 29 2014 - 06:30:03 PST
