[gmx-users] 2019.3 - Fixed Issue 2953: With DD, all intermolecular interactions were ignored?
mark.j.abraham at gmail.com
Tue Jun 18 17:09:56 CEST 2019
Sorry, that's not great wording on our part, I'll fix it. As Eiso said,
only simulations using the [ intermolecular_interactions ] are affected
On Tue., 18 Jun. 2019, 16:44 Eiso AB, <eisoab at gmail.com> wrote:
> Hi Mateusz,
> The intermolecular interactions meant here are the one that can be
> specifically defined as
> [ intermolecular_interactions ] in the topology (e.g. used to define
> distance restraints, between different molecules, see the manual).
> So you shouldn't have to worry about the general intermolecular
> interactions like vdW electrostatics etc.
> On Tue, Jun 18, 2019 at 3:04 PM Mateusz Bieniek <bieniekmat at gmail.com>
> > Dear Developers,
> > I have read your latest release and I cannot work out how it affected my
> > simulations. The overall description is very general and implies that all
> > simulations done with 2019.0-2 should be discarded. If I
> > understand correctly, most of the simulations run nowadays use domain
> > decomposition (DD), and this is your official statement: "when running
> > domain decomposition, all intermolecular interactions (when present) were
> > ignored".
> > However, in the issue 2953, Berk says "You can run with -ntmpi 1 for the
> > moment (or apply the fix)". Does this affect only Gromacs compiled
> > separate MPI library? Can you comment on how the community was affect by
> > this?
> > My next question is about the software development practises. If this is
> > true that it is a very basic error, how is it possible that the test
> > did not detect this? Are not intermoecular interactions the most basic
> > interactions that you would expect gromacs to calculate?
> > Regards,
> > Mateusz Bieniek
> > --
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