RE: Alchemical FEP tutorial files

From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Thu Oct 07 2010 - 09:35:31 CDT

Hi again,
I appreciate that the tutorial is written for experienced users of NAMD, and I have indeed completed the tutorial for the aforementioned program, but this does not change the fact that the FEP tutorial is not very logical in the way it expounds the guidance. It is hard both for me and my supervisor to know exactly what is being meant.

Christian

________________________________________
From: JC Gumbart [gumbart_at_ks.uiuc.edu]
Sent: Thursday, October 07, 2010 1:36 PM
To: 'Chris Harrison'; Christian Jorgensen
Cc: namd-l_at_ks.uiuc.edu
Subject: RE: namd-l: Alchemical FEP tutorial files

Please also note that the latest version of the tutorial can be found here: http://www.ks.uiuc.edu/Training/Tutorials/#freeenergymethods

________________________________________
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Chris Harrison
Sent: Thursday, October 07, 2010 7:23 AM
To: Christian Jorgensen
Cc: namd-l_at_ks.uiuc.edu
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.

Best,
Chris

________________________________________
On Thu, Oct 7, 2010 at 6:55 AM, Christian Jorgensen <christian.jorgensen_at_merton.ox.ac.uk<mailto:christian.jorgensen_at_merton.ox.ac.uk>> wrote:
Hi all,
I am trying to systematically follow the latest version Alchemical FEP tutorial on http://www.ks.uiuc.edu/~char/tutorials/FEP/tutorial-FEP.pdf 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?

./FEP-files/vanilla/alchemy.conf
./FEP-files/vanilla/equilibrate.conf
./FEP-files/vanilla/minimize.conf

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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