[gmx-users] molecule order optimization?

Erik Lindahl lindahl at stanford.edu
Tue Feb 25 09:11:18 CET 2003

Hi Michael,

Future versions will probably have dedicated loops for 4 & 5 particle 
waters, but for
3.1.x you can get a slight speed improvement from the general solvent 
loops by
ordering your waters so that atoms with LJ+Coulomb come first, then 
atoms with
coulomb only and finally atoms with LJ only.



On Tuesday, Feb 25, 2003, at 00:07 US/Pacific, Michael Shirts wrote:

> So, I'm running a box of tip4p waters, using the 3.1.4-included 
> tip4pgmx.itp
> file.  I get the warning:
> The order in molecule 0 could be optimized for better performance
> The order in molecule 1 could be optimized for better performance
> The order in molecule 2 could be optimized for better performance
> .
> .[and so forth]
> .
> (More than 10 molecules where the order can be optimized)
> I've experimented changing the order in the .gro files, but that 
> doesn't seem
> to do anything.  For four (and five) point solvent molecules, is there 
> a "good
> order" that will optimize performance? If so, does one need to change 
> the .itp
> file?  Or does this warning just pop up when using a non-three point 
> water?
> Thanks,
> Michael Shirts
> Stanford Chemistry Department
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