1GROMACS 2021.1 release notes
2----------------------------
3
4This version was released on March 8th, 2021. These release notes
5document the changes that have taken place in GROMACS since the
6previous 2021 version, to fix known issues. It also incorporates all
7fixes made in version 2020.6 and earlier, which you can find described
8in the :ref:`release-notes`.
9
10.. Note to developers!
11   Please use """"""" to underline the individual entries for fixed issues in the subfolders,
12   otherwise the formatting on the webpage is messed up.
13   Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
14   a space between the colon and number!
15
16Fixes where mdrun could behave incorrectly
17^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
18
19Fix MiMiC with virtual sites
20""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
21
22It is likely that MiMiC with virtual sites has not worked
23correctly because the call to construct the sites was placed
24after the call that uses the sites. Now it should work, but we have not tested that it does.
25
26:issue:`3866`
27
28Fix mass perturbation to dH/dlambda
29"""""""""""""""""""""""""""""""""""
30
31The contribution for perturbed mass was missing in dH/dlambda.
32Note that this contribution was not missing from the foreign energy
33differences used for the Bennett acceptance ratio method.
34
35:issue:`3943`
36
37Running AWH with a convolved potential and an FEP dimension gives wrong results.
38""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
39
40The output PMF is wrong when using awh-potential = convolved with a
41pull dimension combined with an FEP dimension. The FEP dimension
42always uses an umbrella potential and the combination does not work
43properly. This has been disabled in grompp.
44
45:issue:`3946`
46
47Remove velocity from partially frozen atoms in md-vv
48""""""""""""""""""""""""""""""""""""""""""""""""""""
49
50md-vv would add some velocity to the frozen dimensions of partially
51frozen atoms during constraining. This did not lead to wrong
52trajectories, as the frozen dimensions of the positions are kept fixed
53during propagation. The non-zero velocities were, however, reported in
54trajectories and final configurations. They might also have lead to
55slightly wrong kinetic energies, since the reported kinetic energy is
56calculated after the velocities are constrained. All effects are
57expected to be relatively small, since they did not accumulate, as the
58velocities were regularly reset to zero once per step.
59
60:issue:`3849`
61
62Fixes for ``gmx`` tools
63^^^^^^^^^^^^^^^^^^^^^^^
64
65Fix periodic boundary conditions in analysis framework tools
66""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
67
68There was a bug in the trajectory analysis framework which caused
69molecules that were broken over PBC not to be made whole. This would
70usually lead to obviously incorrect outliers in analysis output.
71
72:issue:`3900`
73
74Fix range checking bug in ``gmx covar``
75"""""""""""""""""""""""""""""""""""""""
76
77A check was inverted causing range checking to be applied wrong.
78
79:issue:`3902`
80
81Fix various bugs in ``gmx xpm2ps``
82""""""""""""""""""""""""""""""""""
83
84Numerous minor issues were introduced in refactoring since
85|Gromacs| 5.1, now fixed.
86
87:issue:`3881`
88
89Fixes that affect portability
90^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
91
92Fixed compilation on Cygwin
93"""""""""""""""""""""""""""
94
95A |Gromacs| header file was not including the necessary standard
96header. A problem with the ``M_PI`` math constant defined only by
97POSIX and not by C++ was also worked around.
98
99:issue:`3890`
100
101Improve grompp checks of AWH settings when sampling an FEP dimension
102""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
103
104Ensure that the AWH sampling interval is compatible with nstcalcenergy
105when sampling an FEP dimension using AWH. This avoids crashes in the
106first AWH sampling step (step > 0) if the settings were not correct.
107
108:issue:`3922`
109
110Miscellaneous
111^^^^^^^^^^^^^
112* Updated |Gromacs| logos
113