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? 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. 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
