Alchemical FEP calculations in NAMD

From: Satyavani Vemparala (vani_at_VITAE.CMM.UPENN.EDU)
Date: Fri Feb 20 2004 - 22:09:43 CST


I am new to FEP calculations. I have a question:

1.I understand from the tutorial (on NAMD website) that to include the
excluded atoms info into PSF files, CHARMM is used. Is this still the only
way? I do not have access to CHARMM.

2. How is FEP file generated? any software?

3. Any review articles (recent) that would be useful to me to better
understand these calculations?


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