Alchemical FEP tutorial files

From: Christian Jorgensen (
Date: Thu Oct 07 2010 - 06:55:09 CDT

Hi all,
I am trying to systematically follow the latest version Alchemical FEP tutorial on currently in section 1.2 Ethane-to-ethane "zero-sum" transformation: Running the free energy calculation.

It reads "The traditional MD section of the NAMD configuration file could be written for an MD run a constant temperature of 300 K and pressure of 1 bar, using the particle-mesh Ewald (PMD) electrostatics. Set the rigidBonds option to all and choose a time step of 2fs ..... or use the provided restart files from an equilibration run"

Question 1: Does this mean I should build my own configuration file or do I use the ones located in the vanilla directory?

Question 2: Why does the Vanilla directory exist independently of the respective directories of the individual sections of the tutorial, I.e. why are these files not placed in the ./FEP-files/01.ethane-ethane/ directory?

Later on it reads: "Run the forward and backward simulations using, e.g., the commands
namd2 forward-noshift.namd > forward-noshift.log
namd2 backward-noshift.namd > backward-noshift.log"

Question 3: Where are the files forward-noshift.namd and backward-noshift.namd? Am I supposed to write these mylself?

Thank you very much in advance,

Christian Jorgensen,
Merton College, Oxford / PTCL

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