[gmx-developers] Water innerloop
leafyoung81-group at yahoo.com
Tue Feb 28 16:16:45 CET 2006
Thanks, Eric and Mark.
Erik Lindahl wrote:
>> 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
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
And why there is no 110, or 200, etc?
> 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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