On 5/01/2011 5:53 AM, Elton Carvalho wrote:
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
constraints.
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?
Most definitely. Typical GROMACS simulations report up to a few percent
of the total simulation time is spent in dealing with constraints. If
the use of constraints permitted a 2fs timestep rather than 0.5fs, then
it's nearly a four-fold speed-up.
Any other reason I failed to notice?
I seem to recall that bond constraints are held to model the essential
QM nature of interatomic bonds better than a Morse or harmonic potential
(particularly for bonds to hydrogen). I don't recall a reference for
that offhand, unfortunately. Perhaps the original SHAKE paper.
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.
Various coarse-graining approaches exist to take advantage of that kind
of saving, but they also gain from the higher maximum time step.
Mark
My molecular dynamics background is based on Cerius2, so please pardon
some lack of intimacy with GROMACS behaviour.
Regards,
--
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