1GROMACS 2019.1 release notes 2---------------------------- 3 4This version was released on February 15, 2019. These release notes 5document the changes that have taken place in GROMACS since the 6initial version 2019, to fix known issues. It also incorporates all 7fixes made in version 2018.5 and earlier, which you can find described 8in the :ref:`release-notes`. 9 10Fixes where mdrun could behave incorrectly 11^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 12 13Fix error with 2D/3D dynamic load balancing 14""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 15 16With 2D or 3D domain decomposition with dynamic load balancing, 17mdrun would exit with the error "The domain decomposition grid 18has shifted too much .." when a cell size was limited. 19 20:issue:`2830` 21 22.. _release-notes-2019-1-gpu: 23 24Fix incorrect LJ repulsion force switching on GPUs 25""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 26 27When using a CUDA or OpenCL GPU, the coefficient for the second order 28term for the LJ repulsion in the force switching function, called 'A' 29in the manual, had the wrong sign. This lead to very small errors in 30the forces and the pressure. Note that the dispersion force switching 31was correct. The effects of this bug on any physical results seems to 32be negligible. Note that force switching is usually only used in 33combination with the CHARMM force field. 34 35:issue:`2845` 36 37 38Fix segmentation fault in mdrun with domain decomposition 39""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 40 41:issue:`2813` 42 43Fix segmentation fault with energy minimization with the group scheme 44""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 45 46Using energy minimization in combination with the group cutoff scheme 47and domain decomposition could lead to a segmentation fault. 48 49:issue:`2813` 50 51Correct free-energy Delta H output with mass lambda's 52""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 53 54When separate lambda parameters were used for perturbed mass 55free-energy contributions, these contributions were double counted 56in the Delta H output used for BAR calculations. Note that dH/dlambda 57was always correct 58 59:issue:`2703` 60:issue:`2849` 61 62Prevent mdrun -rerun from writing incorrect free-energy output 63""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 64 65Now mdrun -rerun exits with a fatal error when masses or constraints 66are perturbed. Their contributions to Hamiltonian differences and 67derivatives were incorrectly set to zero in version 2019. 68 69:issue:`2849` 70 71Fix possible division by zero in enforced-rotation code 72""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 73 74:issue:`1431` 75 76Fixes for ``gmx`` tools 77^^^^^^^^^^^^^^^^^^^^^^^ 78 79Fix trjconv -ndec 80""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 81 82This only works for writing .xtc files. The code and documentation now 83works correctly with .gro files, which was changed in 2016 release series so that 84it would only write fixed-width columns. 85 86:issue:`2824` 87:issue:`2037` 88 89Fix using index file groups when .tpr file not supplied 90""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 91 92Selections that use groups from a supplied index file can 93again be used even when a .tpr file is not supplied. 94 95:issue:`2847` 96 97Fix tune_pme 98""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 99 100The tool did not work due to a file reading error that is fixed now. 101 102:issue:`2827` 103 104Fixes that affect portability 105^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 106 107With MSVC, disabled internal clFFT fallback used for OpenCL support 108""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 109 110GROMACS requires MSVC 2017, and the GROMACS OpenCL build requires 111clFFT. If clFFT is found on the user's system, then all may be well, 112but the version of clFFT bundled within GROMACS cannot be built 113because only MSVC 2010 is supported by clFFT at this time. A 114configure-time fatal error is now issued in this case. 115 116:issue:`2500` 117 118Explicitly require 64-bit platforms for OpenCL 119""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 120 121A 64-bit OpenCL runtime is required by GROMACS. 122All known OpenCL implementations on 64-bit platforms are 64-bit 123(and there are no known 32-bit platforms with 64-bit OpenCL), 124hence we require a 64-bit platform at configure-time in OpenCL builds. 125A known unsupported 32-bit platform is ARMv7. 126 127Miscellaneous 128^^^^^^^^^^^^^ 129 130Improved docs for applying electric fields 131""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 132