[gmx-developers] Water innerloop

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 28 07:14:27 CET 2006

Yang Ye wrote:
> Hi, Mark
> This is from CHARMM22 paper (JPC, B, 1998, 102: 3586) page 3588
> The water model used in all calculations is the TIP3P model (20) 
> modified for the CHARMM force field.(5) The consistency of the protein 
> and solvent interactions is based on the use of this water model; i.e., 
> it forms part of the system description and other water models would be 
> less appropriate.
> Reference (5) is Reiher, W. E., III. Ph.D. Thesis, Harvard University, 
> 1985. I cannot got it.
> And if you check CHARMM22, 27, HT in TIP3P does have LJ defined, which 
> is different from original TIP3P.

Yep, that's all true, I was wrong.

> So, two questions:
> 1. What's the impact of using original TIP3P water?
> 2. What can be done in GROMACS to accelerate CHARMM's TIP3P water?

Presumably the nonbonded list generation will take care of itself.

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?


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