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

Dallas Warren dallas.warren at monash.edu
Fri Aug 24 05:31:27 CEST 2018

So preparation turns the "warnings" into "notes"?

Sounds like a good idea here. I actually do 6 runs through grompp /
mdrun before my systems are ready for production.  Don't think you
need more flavours than that, though might need one for minimisation?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Fri, 24 Aug 2018 at 08:02, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi,
> 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?
> Mark
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