From: Jun Zhang (coolrainbow_at_yahoo.cn)
Date: Mon Jun 13 2011 - 22:01:59 CDT
I want to use Jarkynski's equation combined with SMD to compute the binding free energy of a protein and its ligand (eg. JCP, 120, 5946). However, I was puzzled by some theoretical issues.
For example, a system composed of water and a ligand. if we move a single ligand in aqueous for some distances, the work done cannot be zero, but the free energy change should be zero since the state of the ligand has not changed.
It seems somewhat strange, and may be a naive question. But I am really puzzled by it, so I'm looking for help. Thank you in advance!
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