Changing functions without recompiling

From: Cole Gleason (
Date: Mon Oct 18 2010 - 16:53:32 CDT

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

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