[gmx-developers] Water innerloop

Erik Lindahl lindahl at sbc.su.se
Tue Feb 28 10:50:08 CET 2006

> Presumably the nonbonded list generation will take care of itself.

Currently the detection of 'water' molecules is performed when  
setting up the forcerecord. If you just modify that you can have any  
type of molecule end up the water or water-water lists.

> Otherwise, modifying the general-case algorithms (for various $x,  
> $y, $z) in gmxlib/nonbonded/nb_kernel_$x/nb_kernel$y$z0_$x.s along  
> the lines of the existing specialisations nb_kernel$y$z[1-4]_$x.s  
> for the specific case of TIP3P in CHARMM is the way forward.  
> Obviously the mechanism that chooses which nb_kernel function to  
> call would need to be expanded.
> Would that be all that's necessary?

Yes, in principle. However, if you only do it in C or Fortran the non- 
water Gromacs assembly loops will probably still be faster.

You won't gain quite as much as for normal TIP3P/SPC/TIP4P either,  
since you're performing more calculations per coordinate load/force  



Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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