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