editing the code of the non bonded pair potentials

From: Asaf Farhi (asaf.farhi_at_weizmann.ac.il)
Date: Fri Aug 30 2013 - 04:27:19 CDT

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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