alchemify FEP

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Thu Feb 17 2005 - 13:14:20 CST

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Hi,all,

I am using alchemify FEP in NAMD to calculate free energy difference before and
after mutating a residue in a peptide chain. However, I found that only VDW and
electrostatic energy are included in the calculation of free energy. Why we
do not need care about kinetic energy, bond stretching, etc. Who have any ideas?

Regards,

Wei Chen

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