[gmx-users] Constraints and efficency

Elton Carvalho eltonfc at if.usp.br
Tue Jan 4 19:53:59 CET 2011

Hello, fellow GROMACS users!

I noticed many users applying constraints to their simulations, be it
SETTLE to water molecules or LINCS to some other species. This brings
about an efficiency concern once that after each Verlet step some
systems of coupled equations must be solved in order to apply these

My question is: water molecules are the most numerous species in a
solvated simulation, and the SETTLE algorithm seems to take O(n) time
for each molecule (Hence, O(3) per molecule), thus yelding O(M) to
apply SETTLE to all M water molecules in a system, per MD step. Why is
this beneficial? Does the larger timestep allowed by eliminating
high-frequency O-H vibrations outweigh the time needed by SETTLE? Any
other reason I failed to notice?

Same thing for LINCS in, say, surfactant molecules: Is there any other
reason to do this other than shave off higher frequencies (C-H for
instance) and allow a larger timestep?

The only reason I see to constrain movement other than that fraquency
shaving (and, of course, isolating some behaviour of interest, but
this is case-specific) would be to reduce the number of dimensions of
the phase space and save computatuon time, but, as implemented, this
doesn't seem possible with the code as is.

My molecular dynamics background is based on Cerius2, so please pardon
some lack of intimacy with GROMACS behaviour.

Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil

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