Re: WCA Particle

From: Peter Freddolino (
Date: Thu Jul 10 2008 - 11:25:51 CDT

Hi Dave,
if you're feeling adventurous, we have some tabulated potential code
that does exactly what you describe (spline lookup table). I will send
you the code off-list so you can try it out. It's still being shaken a
bit more before being added to cvs.


Dave Rogers wrote:
> Dear NAMD gurus,
> I want to simulate a large protein system and include a
> Weeks-Chandler-Anderson (WCA) particle. This would involve adding an
> atom to my topology which interacts with other atoms using a shifted
> LJ potential out to the minimum, at which point it becomes zero.
> Gromacs has a "read pairwise potential from file" option that has
> allowed me to do this in the past.
> I am thinking I might be able to do the same type of thing in NAMD
> by creating a spline lookup table specifically for this
> WCA-to-everything interaction, but how do I get NAMD to use this table
> instead of the usual one? I have also considered using the tclforces
> scripting interface, but this would require me to check all pairwise
> distances inside of tcl -- which would by about as efficient as
> writing my own MD code (unless I've overlooked something).
> What (if any) is the simplest -- i.e. least code modification -- way
> you can imagine doing this and your estimated difficulty level (in Lt.
> Scotty hours)?
> Thanks,
> David M. Rogers
> PhD Candidate
> Dr. Beck Lab
> University of Cincinnati

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