Re: about the vdw Interpolation calculation in NAMD source code

From: Jim Phillips (
Date: Thu Nov 20 2014 - 08:29:27 CST

What is the functional form (including parameters) of the new LJ potential
you want? If it is A f(r) + B g(r) and you want to replace the existing
LJ potential for all atom pairs then you just change f(r) and g(r) from
r^-12 and r^-6 to your new form, and figure out how to read in your
parameters, which would be somewhat more complex. We might be able to
support this more easily in the future, but it will help to know what
kinds of things people actually want to do.


On Thu, 20 Nov 2014, ¬ wrote:

> Dear all,

I try to modified the namd code to implement a new type force field. I want some help in understanding the nonbonded force calculation like VDW in namd. I have found some local experts, but none of them show interesting in such detail.

The source code involving nonbonded calculation (ComputeNonbondedBase.h ComputeNonbondedBase2.h) show a very abstract interpolation method and a large number of macro definitions, completely beyond my ability to fully understand it.

Could some one give me some hint in how this is realized in namd. For example, using the interpolation to calculate a new LJ potential energy.

Best Regards

¬(YuKun Lu)
Address: Institute of Theoretical Physics, CAS,
                  Zhong Guan Cun East Street 55 #,
                  P. O. Box 2735, Beijing 100190, P. R. China

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