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... >> 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, -- 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
