[gmx-users] Assembly codes

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 17 22:22:30 CET 2005

On Thu, 17 Feb 2005, Manoj wrote:

>I am trying to modify LJ potential in such a way that
>I need to make certain changes in the way gromacs
>calculates LJ interactions. I only need to edit a few
>lines and add a few 'if' statements in the inl0100 and
>inl3030 which is fine as long as I stick to
>"innerc.c". I can successfully change the "innerc.c"
>code and use it after disabling assembly loops. 
>However, without assembly loops, the code runs
>significantly slower. My question is, how are these
>files i.e. x86_sse.s and x86_sse2.s generated ? I
>figured out some stuff about the intel-syntax assembly
>code and the NASM format. Is there an easy way to do
>this? does anyone actually write this? If not, then
>what are the utilities to do this? 

It is hand-written. Can't you use a table potential?

>Could anyone please let me know how to generate these
>assembly codes (x86_sse.s & x86_sse2.s) ?
see above.

>Besides, is there a way to implement WCA potential
>(solute-solute & solute-solvent) in gromacs?
What is that?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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