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 b14188ac9f502f31b8f25b537d3ea1b167de1703 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 35051360c289bd8afc8b39906556d367edc09a2c 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](/uploads/dd686414368936351fce3ef5e19ad6be/pp_0.0005.tpr) NEMD tpr file created with 5.1.5. * [gromacs_2018.4_viscosity_ppm.patch](/uploads/34dad574bd4c0f4393255374c401b073/gromacs_2018.4_viscosity_ppm.patch) Patch * [nvt_vis.mdp](/uploads/82561967d9c5e94e41236a296ff3e395/nvt_vis.mdp) * [a0.gro](/uploads/8175fb29fd200a8a55777c4b29834b37/a0.gro)