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

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 11 13:03:22 CEST 2017


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.


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