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Issue created by Paul Bauer@acmnpvMaintainer

critical box fluctuations when using GPUs - Redmine #2845

Archive from user: Ramon Guixa-Gonzalez

Systems become extremely unstable (i.e. very large box fluctuations) after 80-100 ns until they eventually deform (i.e. membrane
abnormally enlarged, big water pores go through, and protein collapses). None of the following actions helps:

1 - Increase/decrease certain parameters within the mdp file
(e.g. tau-
2 - Re-build and re-equilibrate the system.
3 - Use of different GROMACS versions, namely 5.4, gromacs2016 and
gromacs2018.
4 - Use of different computers and different GPUs models.
5 - Use of a different system (other membrane proteins of the same family with
different ligands).

Sooner or later, same thing happens over and over again in every protein-membrane system. Intriguingly, systems never
crash (i.e. simulations keep on running despite of the observed artifacts).
Thus, the gromacs+CHARMM36+GPUs combination inevitably induces protein-membrane systems to collapse.

The only workaround so far is running the system using only CPUs.

(from redmine: issue id 2845, created on 2019-01-28 by gmxdefault, closed on 2019-09-24)

Fix incorrect LJ repulsion force switching on GPUs

When using a CUDA or OpenCL GPU, the coefficient for the second order
term for the LJ repulsion in the force (not energy) switching function,
called 'A' in the manual, had the wrong sign in both the force-only
kernels and the force+energy kernels.
Note that the dispersion force switching was correct.

Fixes #2845

Change-Id: Ib5c250a1f370d4c0a4fd652bf6efa03e70e18748
  • Revision de27733a by Berk Hess on 2019-02-04T13:26:07Z:
Fix incorrect LJ repulsion force switching on GPUs

When using a CUDA or OpenCL GPU, the coefficient for the second order
term for the LJ repulsion in the force (not energy) switching function,
called 'A' in the manual, had the wrong sign in both the force-only
kernels and the force+energy kernels.
Note that the dispersion force switching was correct.

Cherry-picked from 2019

Fixes #2845

Change-Id: Ib5c250a1f370d4c0a4fd652bf6efa03e70e18748
  • Revision c131d790 by Berk Hess on 2019-02-20T07:59:12Z:
Fix incorrect LJ repulsion force switching on GPUs

When using a CUDA or OpenCL GPU, the coefficient for the second order
term for the LJ repulsion in the force (not energy) switching function,
called 'A' in the manual, had the wrong sign in both the force-only
kernels and the force+energy kernels.
Note that the dispersion force switching was correct.

Cherry picked from 2019

Fixes #2845

Change-Id: Ib5c250a1f370d4c0a4fd652bf6efa03e70e18748
  • Revision 8fc3cc55 by Berk Hess on 2019-09-21T10:01:55Z:
Fix incorrect shift forces for CMAP

The shift force indices were inverted for the second and third
atom in the CMAP term, leading to incorrect virial and pressure
contributions when these atoms resided in different periodic images.

Fixes #2845 and #2867

Change-Id: I1946a1d375d6c62e4e6d23ee25b92b42a3d4a6f7
  • Revision 771d4c99 by Berk Hess on 2019-09-21T10:37:04Z:
Fix incorrect shift forces for CMAP

The shift force indices were inverted for the second and third
atom in the CMAP term, leading to incorrect virial and pressure
contributions when these atoms resided in different periodic images.

Fixes #2845 and #2867

Also prepares branch for another point release.

Change-Id: I1946a1d375d6c62e4e6d23ee25b92b42a3d4a6f7