From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Tue Apr 18 2006 - 11:09:05 CDT
The most expensive part of MD is the force routine. Since you'll still
be calculating the force from the "frozen" atoms, the computational cost
will be just about the same as it would be without frozen atoms.
I suppose that knowing some atoms are frozen could potentially lead to a
different or more efficient parallelization algorithm. But I don't know
how NAMD handles it, and I doubt you'll get a significant speed up.
Jacob Pøhlsgaard wrote:
> Hi people
> I'm looking to simulate a very small area of a very large complex.For
> this I'm going to freeze some residues, restrain others and allow the
> atoms in the area of interest to move freely.
> My question is if anyone knows how much computational cost I have to
> pay by including the whole (~150.000 atoms) complex as frozen atoms?
> Is there some general rule of thumb?
> Is it a good idea to include all the residues at all? I'll have atoms
> way beyond the electrostatic cutoff, but as I understand it, there's
> still a a contribution to electrostatics that far away since I'm using
> the PME method.
> Best regards
> *Jacob Pøhlsgaard*
> Department of Biochemistry and Molecular Biology
> SDU, Denmark
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