RE: Alchemical FEP tutorial files

From: JC Gumbart (
Date: Thu Oct 07 2010 - 07:36:13 CDT

Please also note that the latest version of the tutorial can be found here:



From: [] On Behalf
Of Chris Harrison
Sent: Thursday, October 07, 2010 7:23 AM
To: Christian Jorgensen
Subject: Re: namd-l: Alchemical FEP tutorial files


Dear Christian,


The Alchemical FEP tutorial is considered an advanced level tutorial and as
such users compose their own namd config files using the files in the
vanilla directory as guides/examples.




On Thu, Oct 7, 2010 at 6:55 AM, Christian Jorgensen
<> wrote:

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

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078

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