[gmx-users] runtime statistics

Erik Lindahl lindahl at stanford.edu
Mon Feb 24 23:24:08 CET 2003

Hi Rui,

All the three last lines refer to nonbonded interactions with normal 
Lennard Jones and tabulated Coulomb. The first line is for interactions 
between arbitrary atoms (in most cases protein-protein), the second is 
for interactions between a protein atom and an entire water molecule 
(charge group), and the final line for interactions between two water 

This separation doesn't affect the results; the only reason for the 
separate loops is optimization. Calling the water-water loop is much 
faster than looping over all the water atoms in the normal loop. (Two 
reasons: better cache properties, and we hide the latencies better).



On Monday, Feb 24, 2003, at 14:16 US/Pacific, qiao rui wrote:

> Hi, List:
> 	I am looking at the output of Gromacs (md.log) and get a little
> bit confused over the following message:
> Computing:        % Flop's
> ...
> Coulomb (T)       0.1
> ...
> LJ+Coulomb (T)    0.1
> LJ+Coulomb (T)(W) 1.2
> LJ+Coulomb(T)(WW) 57.8
> ....
> The output says that WW stands for Water-water and T for tabulated. My
> doubt is why there are LJ+Coulomb (T)(WW) and LJ+Coulomb(T)(W): is the
> latter for the interaction between Water the other molecules in the
> system?
> Thanks a lot for your time.
> Rui
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