Re: editing the code of the non bonded pair potentials

From: Axel Kohlmeyer (
Date: Fri Aug 30 2013 - 04:34:46 CDT

On Fri, Aug 30, 2013 at 11:27 AM, Asaf Farhi <> wrote:
> 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.

you did post a mail, but there was no real question in it. why should
somebody reply to that. to get a (good) answer you have to ask better

> Now I don't know what to do.
> Could you please advise me?

pick a different code that is easier for you to understand and modify,
or ask better questions (i.e if you don't describe what exactly you
need to modify, where you already looked and what you tried and how
this modification would be affected by parallel execution).


> Thanks in advance,
> Best regards,
> Asaf

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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