[gmx-users] Trying to use cutoff electrostatics with MARTINI

Graham J.A. J.A.Graham at soton.ac.uk
Tue Apr 11 14:54:37 CEST 2017

Thanks Mark,

That makes sense now then, and explains the very small performance
difference I'm seeing between the two cases when run out for a bit


On Tue, 2017-04-11 at 11:03 +0000, Mark Abraham wrote:
> Hi,
> On Tue, Apr 11, 2017 at 12:09 PM Graham J.A. <J.A.Graham at soton.ac.uk> wrote:
> > 
> > Hi,
> > 
> > I'm preparing to do some benchmarking and wanted to look at the
> > performance differences between reaction-field and cutoffs for the
> > electrostatic model with the MARTINI forcefield.
> > 
> You'd expect that to be small - one can implement plain cutoff as RF with a
> zero parameter.
> > 
> > I've downloaded the recommended MDPs from the MARTINI website, but when
> > I specify cutoff in the MDP I still get "NxN RF Elec. + LJ" in the
> > performance tables at the end of the log.  The section at the top of
> > the log shows that GROMACS has recognised that I'm asking for cutoffs.
> > 
> > This is happening with both GROMACS 2016.3 and 5.1.4.  Am I
> > misunderstanding the log output, or is something going wrong?
> > 
> Particularly on hardware that supports fused multiply-addition (most of the
> current relevant ones), the extra operation is ~free, and the only overhead
> is the load of the constant parameter, which happens outside the inner
> loop, and perhaps some register pressure. So we don't bother with a special
> kernel for this case, and your observations are expected.
> Mark

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