[gmx-users] Feedback wanted - mdp option for preparation vs production

Mark Abraham mark.j.abraham at gmail.com
Fri Aug 24 00:02:39 CEST 2018


In recent years, grompp has grown some more strident warnings that try to
help GROMACS users understand when their .mdp choices might lead to
calculations that are known not to simulate real physics. Berendsen-style
weak coupling algorithms (for either temperature or pressure) are known to
produce the wrong velocity distributions, for example.

Despite this, there are times when one might want to use such an algorithm,
and so we permit users to suppress warnings from grompp with -maxwarn.
However, encouraging such behaviour leads to people abusing -maxwarn, and
we'd all like to avoid that.

One important special case is equilibration, where it is often advisable to
use Berendsen pressure coupling while preparing the system, and then a
different coupling algorithm approach for production simulation. Currently
grompp can't be sure whether its input is intended for production
simulation, or merely preparation for simulation.

Following discussion among some developers, how do people feel about a new
mdp option that permits users to specify e.g. "production" or
"preparation," defaulting to "production." grompp retains its current
warning behaviour for "production," but merely advises about such issues
when preparing systems. Do those names and behaviours seem suitable? Do we
need more flavours of calculation type?


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