[MMTK] Partial energy computation

Dmitriy Morozov mmtk at foxcub.org
Thu Nov 20 23:39:10 CET 2003


As a quick follow-up question to my previous ones, what are the 
units for the energy returned by universe.energy()? Why is it 
that with Amber94ForceField() I'm getting:
-2811.80 + -3049.41 + -209.64 = -6070.85
Time as a whole 3.4856710434
Time for the first set 0.90073800087
Time for the second set 0.905595064163
Time for between the sets 5.10468101501

While with Amber94ForceField(None, {'method': 'multipole'}), I 
get:
2753.09 + 2539.67 + -299.20 = 4993.56
Time as a whole 18.5412820578
Time for the first set 15.5048160553
Time for the second set 12.9431940317
Time for between the sets 19.6578210592

Ignore the timings for now, -6070 and 4993 are quite a bit of a 
difference. Or am I missing something?

Thanks.
Dmitriy


On Wednesday 19 November 2003 03:33 pm, you wrote:
> On Wednesday 19 November 2003 19:25, Dmitriy Morozov wrote:
> > Why does the following happen? When I run the code
> > (attached) the time that it takes to compute the energy for
> > each half of the atoms of the protein is almost the same as
> > for the whole protein, and the time that it takes to compute
> > the energy for
>
> In your script, you calculate each energy only once. In the
> first call for each subsystem, the internal data structures
> (list of bond and angle terms, Lennard-Jones parameters, etc.)
> are set up, which is a rather expensive procedure. What you
> are measuring is probably just that.
>
> To get a more realistic measure for repeated energy
> evaluations, calculate each energy twice in sequence and
> measure the time for the second evaluation.
>
> Konrad.




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