Re: LES : size

From: Leandro Martínez (
Date: Fri Nov 10 2006 - 13:00:53 CST

1) In the manual of NAMD there is now clue about how many atoms can be
included into LES. Is there any limitations and considerations about it ?
I think there is a limitation on the number of copies of the LES molecule
(or atom), but
not on the number of atoms of this molecule.

2) How calculation time depends on number of atoms and number of copies ?
The greter the number of copies, the greater the number of atoms of the
so the calculation time should increase. However, when the number of copies
is increased, the barriers for, lets say, dissociation, get smaller, and the
should be observed more rapidly (thats the point of LES). Therefore, you
save time as more copies you put, but the precision of the may be worst.

On the other hand, I don't know which is the effect of the number of copies
in computation time for paralell computations. How is the partition of the
done? Good question. Because since several copies may share the same
region of the space, the partition for distributed computing may get
Is that true?

3) Is it effective for crossing enthalpic barriers, or entropy barriers, or
both ?

Yes, it is effective, but it is an approximation and, as such, have some
You could check some studies done with, and the theoretical studies,
the ones done by Straub and Karplus, in which the limitations and advantages
of the technique are well discussed.


Leandro Martinez
Institute of Chemistry
State University of Campinas, Brazil
Initial configurations for molecular dynamics:
Convergent algorithms for protein alignment:

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