1/viscosity output is wrong in gmx-2018.2, but OK in gmx-5.1.5 - Redmine #2572

Archive from user: Sun Tiedong

When calculating viscosity with periodic perturbation, the output average value of 1/viscosity in 2018.2 is around zero. The NEMD is set up in NVT ensemble. Only “cos-acceleration” is set, instead of “acc-grps” and “acceleration” in .mdp file. The same tpr file works with gmx-5.1.5, i.e. gives value in reasonable range.

Both versions of gromacs are compiled on CentOS 7, with gcc-7.3.1/or gcc-4.8.5, cuda-9.2, with the following cmake command:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on

(from redmine: issue id 2572, created on 2018-07-12 by gmxdefault, closed on 2018-12-22)

Changesets:
- Revision b14188ac by Jiannan Liu on 2018-12-19T15:12:50Z:

Missing factor of 2 in cos-acceleration

The bug was introduced in commit 69470fc4e9fd990eb53b22c17dc7a699c583d126

Last working version is 2016.5

Affected 2018 and 2019

Fixes #2572

Change-Id: Ibad31b0d8cec7c5f4b77a73b1fbab0ff114b50b6

Revision 35051360 by Jiannan Liu on 2018-12-22T01:24:39Z:

Missing factor of 2 in cos-acceleration

The bug was introduced in commit 69470fc4e9fd990eb53b22c17dc7a699c583d126

Last working version is 2016.5

Affected 2018 and 2019

Fixes #2572

Change-Id: Ibad31b0d8cec7c5f4b77a73b1fbab0ff114b50b6

Uploads:
- pp_0.0005.tpr NEMD tpr file created with 5.1.5.
- gromacs_2018.4_viscosity_ppm.patch Patch
- nvt_vis.mdp
- a0.gro