how to do free energy perturbation calculation in NAMD?

From: jz7_at_duke.edu
Date: Tue Feb 07 2006 - 11:21:39 CST

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Dear all,

I am following the tutorial for setting up alchemical free energy
perturbation calculation in NAMD. However, it's still not clear to me how
to actually run the calculation. Here are my questions.

First, how should I define the dual-topology if the residues (RESI)
involved are identical before & after the alchemical transformation, but
the patch residues (PRES) are different?

Second, what is the complete NAMD script for the free energy perturbation
calculation? I think in the turtorial, it only shows the "FEP" part.

Thanks a lot!

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