Re: about the vdw Interpolation calculation in NAMD source code

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Thu Nov 20 2014 - 08:20:54 CST

Hi,

I'm not sure what kind of nonbonded forces you want to implement, but
you may be able to do it through the tabulatedEnergies feature
(without modifying NAMD's code). With it, you can do anything that's
spherically symmetric:

http://www.ks.uiuc.edu/Research/namd/2.10b2/ug/node23.html

A viable option if your custom forces apply to only a small part of
the system is TclForces. But it's likely to be slow if you need the
forces on every atom.

http://www.ks.uiuc.edu/Training/Tutorials/science/forces/forces-tutorial-html/node2.html

Calculating the nonbonded forces is the most expensive part of the
NAMD code, which in turn makes it the most optimized and probably the
hardest to understand. You should avoid having to edit it if you can.

Regards,
Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Thu, Nov 20, 2014 at 2:44 AM, ε’η¦Ήι”Ÿ <luyukun_at_itp.ac.cn> 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
>
>
>
>
>
> --
> ε’η¦Ήι”Ÿ(YuKun Lu)
>
> Address: Institute of Theoretical Physics, CAS,
> Zhong Guan Cun East Street 55 #,
> P. O. Box 2735, Beijing 100190, P. R. China
>
> Email：lcyqky_at_Gmail.com
> luyukun_at_itp.ac.cn
>

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