[gmx-developers] Water innerloop

Yang Ye leafyoung81-group at yahoo.com
Tue Feb 28 16:16:45 CET 2006

Thanks, Eric and Mark.

Erik Lindahl wrote:
> Hi,
>> 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.
I have identified this code in gromacs source. The criteria for water 
innerloop is stated in manual B.2.1. I see that CHARMM TIP3P does not 
fulfill the requirements. Get the TIP3P-SPC water inner loop to run for 
CHARMM TIP3P will not produce desired results. This is what I have 
>> Would that be all that's necessary?
> 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.
> 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 
> store.
A general question towards GROMACS source. May I know which kernel is 
used for a system contains CHARMM TIP3P?
For example, for SSE, what does "No Coul" in 010 (No Coul, vdw=L-J, no 
water optimization) mean? Does it imply that it is for system without 
coulomb interactions?

And why there is no 110, or 200, etc?
> Cheers,
> Erik
> -----------------------------------------------------------
> 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 
> Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
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