[gmx-users] Force Calculation

Justin M. Shorb shorb at wisc.edu
Wed Jun 28 23:55:37 CEST 2006


I have managed to hack through all the Gromacs code and at the bottom 
of it all are machine-run look up tables. Does anyone know of where I 
can find the organization of these tables and the way they are called 
through the program? Or possibly, if anybody has written their own code 
to extract data from the look-up tables on the fly? Luckily, Gromacs 
has already sorted out the different contributions to the forces so I 
think I can pull out the data I need, but I'm afraid I don't even know 
what sort of files (or code) the table functions are written in.

Where I've gotten is to: /src/gmxlib/nonbonded/nonbonded.c  which calls 
the machine specific kernels. I am more than willing to work through 
this myself, but can anybody point me to a good book/site that explains 
what is actually going on when Gromacs looks up these forces?

Sorry for the imprecise language! Basically I just need to extract the 
SR electrostatic force from the look-up tables on the fly, and can't 
find any references out there that explain what goes on in nonbonded.c

Thanks in advance,

Justin M. Shorb			Phone: (608) 262-0483
Skinner Group				shorb at wisc.edu
University of Wisconsin-Madison,  Department of Chemistry
1101 University Ave., Madison, WI, 53706

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