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