[gmx-users] 2019.3 - Fixed Issue 2953: With DD, all intermolecular interactions were ignored?

Eiso AB eisoab at gmail.com
Tue Jun 18 16:44:35 CEST 2019

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 with
> 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 without
> 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 cases
> 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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