did not affect the, usual, setup where charges or atom types are actually
perturbed.
-:issue: `2640`
+:issue:`2640`
Add constraint contribution to foreign Hamiltonian differences
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Hamiltonian values. This is important for free energy calculations,
such as BAR.
-:issue: `2703`
+:issue:`2703`
Add mass contribution to foreign Hamiltonian differences
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For free energy calculations with perturbed masses, the kinetic energy
contribution was missing from the foreign Hamiltonian values.
-:issue: `2703`
+:issue:`2703`
Work around bugs with expanded ensemble runs
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
other integrators when nstexpanded was not a multiple of nstcalcenergy.
In these cases mdrun now sets nstcalcenergy to 1.
-:issue: `2714`
-:issue: `2718`
+:issue:`2714`
+:issue:`2718`
Checkpoint continuations require suitable .tpr files
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Use gmx grompp or gmx convert-tpr to make a .tpr file that expresses
the intent.
-:issue: `2717`
+:issue:`2717`
Fixes for ``gmx`` tools
^^^^^^^^^^^^^^^^^^^^^^^
PME grids with size along Z larger than 511 would make mdrun exit
with a cryptic CUDA error.
-:issue: `2779`
+:issue:`2779`
Fix LINCS accuracy with OpenMP when constraint triangles are present
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
when the last OpenMP thread has at least one such triangle. This would
cause a slight loss of accuracy in inhomogeneous systems.
-:issue: `2808`
+:issue:`2808`
Fix acceleration with ``cos-acceleration``
""""""""""""""""""""""""""""""""""""""""""
A factor of 2 was missing from the acceleration value, leading to incorrect
results when e.g. calculating viscosities.
-:issue: `2572`
+:issue:`2572`
Fix checkpoint restart of tpr with infinite step count
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works correctly with .gro files, which was changed in 2016 release series so that
it would only write fixed-width columns.
-:issue: `2813`
-:issue: `2037`
+:issue:`2813`
+:issue:`2037`
Fixes to improve portability
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
the two coupling times involved are similar. Now grompp warns when ``tau-p``
is less than two times ``tau-t``.
-:issue: `2749`
+:issue:`2749`
Fixed efficiency issue with shell code minimization
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Code cleanup touching unnecessarily complex code created an efficiency
issue. Both the issue and some of the complexity are now fixed.
-:issue: `2705`
+:issue:`2705`
Added code generation support for NVIDIA Turing GPUs
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