From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Oct 19 2010 - 11:56:40 CDT
There is a new, undocumented tabulated energies capability in NAMD 2.7
that was added to support coarse-grained models by replacing the
Lennard-Jones potential (electrostatics is unchanged). The options are
tabulatedEnergies, tabulatedEnergiesFile, and tableInterpType. You'll
have to take a look at the source code (Parameters.C) to see how it works.
On Mon, 18 Oct 2010, Cole Gleason wrote:
> Hello all,
> Just as a disclaimer, I would like to say I have no idea how NAMD works
> beyond simple simulations. I also have no real knowledge of C, although
> someone on my team has some. The extent of my programming expertise is a
> bit of Python and some Ruby. Since that is out of the way, here is my
> I am a high school senior working with a few other students and my professor
> on some Molecular Dynamics research. I'm handling the admin side of things
> by building and keeping our small cluster running. What my professor wants
> to do is be able to change the functions and parameters of the pairwise
> interactions in simulations. While I don't think that is too hard, the
> problem is that he wants to do this without recompiling the code every time.
> He gave me some kind of Fortran90 function parser one of his friends wrote
> and wants me to allow the function parser to feed the equations to NAMD.
> The function parser seems to take a function string and create an internal
> representation of the function. My professor suggested we use some kind of
> C library to call the fortran code.
> Now, I think this is the wrong approach. It seems that even if this is
> possible, the performance hit will be significant. Someone told me that I
> should instead just rewrite the parts of the NAMD source code (or CHARMM
> perhaps?) we want to change and then somehow just recompile those sections.
> Is that possible? How do I go about doing that?
> Obviously this post is a little vague, so please tell me if you need any
> more information. Thanks in advance to anyone who responds.
> Cole Gleason
> Student, Marmion Academy
> Email: cole_at_colegleason.com
> Website: colegleason.com
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