[gmx-users] Help on MD performance, GPU has less load than CPU.

[Mark Abraham]

Hi,

Sure. But who has data that shows that e.g. a free-energy calculation with
the defaults produces lower quality observables than you get with the
defaults?

Mark

On Wed, Jul 12, 2017 at 5:59 PM Téletchéa Stéphane <
stephane.teletchea at univ-nantes.fr> wrote:

> Le 11/07/2017 à 15:24, Mark Abraham a écrit :
> > Guessing wildly, the cost of your simulation is probably at least double
> > what the defaults would give, and for that cost, I'd want to know why.
>
> Estimated colleague,
>
> Since this is a wild guess, I'd think to add some guesses myself. I
> remember "some time" back having used a lower tolerance on Ewald for
> amber simulations (around amber 4/5/6 ...) and it was more common at
> this time I presume. This may also be linked to the fact that amber has
> a short cut-off at 8 angstrom for electrostatics ...
> Someone apparently "ill" at the time already found this stane in 2009:
>
>
> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/vTjpMdwU/gromacs-preformance-versus-amber
>
> Out of my memroy, I remembered using 10-6 for Ewald tolerance in AMBER,
> and this is mentioned here:
>
> http://ambermd.org/Questions/ewald.html
>
> ... apparently linked to DNA simulation as found in JACS 117,4193 (1995)
>
> In short, this value may come in back and forth for "historical" reasons
> (and misuse, of course).
>
> Others may have additional comments :-)
>
> Best,
>
> Stéphane
>
>
> --
> Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
> Design In Silico
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