FW: editing the code of the non bonded pair potentials

From: Asaf Farhi (asaf.farhi_at_weizmann.ac.il)
Date: Fri Aug 30 2013 - 04:31:44 CDT

The second one is at:
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Asaf Farhi [asaf.farhi_at_weizmann.ac.il]
Sent: Friday, August 30, 2013 12:27 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: editing the code of the non bonded pair potentials

Dear NAMD developers

Hi. My name is Asaf.

In the last two years I've been working on methods for calculating free energy differences.
I have worked on the first method that is aimed for MC simulations.
The article on the first method was published:

I then worked on another method that is aimed for MD simulations.
The article is at:

I submitted the 2nd article and the referees asked to add a MD demonstration.
I decided to implement it using NAMD and studied the software for a week.
Then I simulated phenol in water.
Now I need to very slightly edit the code in order to implement the method but I don't know where in the code is the relevant place.
I posted on the mailing list the question but so far without reply.
Now I don't know what to do.
Could you please advise me?

Thanks in advance,
Best regards,

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