On 2011-01-05 21.44, Elton Carvalho wrote:
On Tue, Jan 4, 2011 at 7:38 PM, Mark Abraham<mark.abra...@anu.edu.au> wrote:
On 5/01/2011 5:53 AM, Elton Carvalho wrote:
[...] 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.
Thanks :)
So, the larger ts allowed would be indeed the main reason to apply
constraints...
No! Harmonic bonds are not good either. This is described in chapter 1
of the manual.
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.
Ok, I'll take a look at those papers, thank you
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.
Oh, yes, coarse-graining methods definitely reduce the complexity of
the system, but I was focusing on all-atom simulations in my message.
Again, thank you for your response,
Best regards,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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