Thank you very much for the answer. On Tue, Nov 18, 2014 at 2:03 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> On Tue, Nov 18, 2014 at 7:38 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > > > Hi. > > > > from online manual: > > > > "*ewald-rtol (1e-5)* The relative strength of the Ewald-shifted direct > > potential at *rcoulomb* is given by *ewald-rtol*. Decreasing this will > give > > a more accurate direct sum, but then you need more wave vectors for the > > reciprocal sum." > > > > Is it ok to use ewald-rtol=1e-9 for Amber99SB-ILDN forcefield? > > > > That's not a question that has a useful single answer. > 1) It wasn't parameterized with any Ewald method, so any subsquent use of > that method is valid only upon empirical evidence. > 2) Different observables in different systems have different dependencies > on the quality of the electrostatics model, and this one parameter is only > part of any story. > 3) A tiny magnitude of forces at the cutoff matters little if they're being > added to other forces at shorter distances - and if there's more than about > 5 orders of magnitude difference, then the small ones get lost in the > accumulation in floating-point representation > 4) Making one part of the electrostatics approximation super accurate while > ignoring the other doesn't do any good when you add them together, because > the largest error dominates. > 5) Some other error might be more dominant still (e.g. incomplete sampling, > interior residues have the same charges as exterior residues, no > polarizability) > > Will the sum in reciprocal space become very inaccurate? > > > > Yes, like the docs say, because ewald-rtol and rcoulomb are used to compute > the Ewald splitting parameter beta, which is then used in reciprocal space > also. > > Or this will just make the simulation run slower? > > > > By itself, it's just multiplication by a different scaling factor. Fixing > the issues in reciprocal space (increasing number of grid points and/or > spline interpolation order) will be expensive. > > Mark > > > > Thanks again. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.