1GROMACS 2019.4 release notes 2---------------------------- 3 4This version was released on October 2nd, 2019. These release notes 5document the changes that have taken place in GROMACS since the 6previous 2019.3 version, to fix known issues. It also incorporates all 7fixes made in version 2018.7 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 incorrect pressure when atoms in CMAP cross a box boundary 20"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 21 22The virial calculation and thus the pressure would be incorrect 23when the second and third atom involved in a CHARMM CMAP correction 24term would reside in different periodic images. This can happen when 25a protein is positioned over a box boundary. Note that the energy 26and forces were correct, but sampling was affected when pressure 27coupling was applied when a protein crossed a box boundary. 28 29:issue:`2845` 30:issue:`2867` 31 32Fix incorrect LJ cut-off on GPU when rvdw < rcoulomb 33"""""""""""""""""""""""""""""""""""""""""""""""""""" 34 35When rvdw was chosen by the user to be smaller than rcoulomb in the mdp file, 36the LJ cut-off would initially be set to the Coulomb cut-off for computing 37non-bonded interactions on the GPU. This only affected energy minimization, 38mdrun -rerun and the first 2*nstlist steps of a normal MD run, since the correct 39LJ cut-off is set when PME tuning (on by default) starts after 2*nstlist steps 40(unless PME tuning was disabled with -notunepme). 41 42:issue:`3056` 43 44 45Fix (unlikely) missing bonded forces with CUDA GPUs and domain decomposition 46"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 47 48Forces could be missing for bonded interactions computed on CUDA GPUs with 49domain decomposition when there are non-local bonded interactions, but no 50non-local non-bonded interactions between two domains. Note that this is 51extremely unlikely to happen, since the distance between the bonded atoms 52needs to be larger than the pair-list cut-off distance and there should be no 53other non-local atoms within the pair-list cut-off distance. 54 55:issue:`3063` 56 57Fix incorrect reporting of final kinetic energy and temperature 58""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 59 60With the leap-frog integrator, the kinetic energy and temperature reported 61for the last step were incorrect when the last step was not divisible by 62nstcalcenergy, nsttcouple or nstpcouple. 63 64:issue:`2950` 65 66Fix segmentation fault in grompp and mdrun with cosine COM pulling 67"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 68 69:issue:`3023` 70 71 72Fixes for ``gmx`` tools 73^^^^^^^^^^^^^^^^^^^^^^^ 74 75Fix grompp not adding angle constraints between constraints 76""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 77 78When using the mdp option constraints=all-angles, angles involving 79bonds supplied as constraints in the topology would be removed, 80but not replaced by angle constraints. 81 82:issue:`3067` 83 84Fix gmx wham with angle and dihedral geometries 85""""""""""""""""""""""""""""""""""""""""""""""" 86 87gmx wham would apply an incorrect radian to degree unit conversion, 88leading to no overlap or not-a-number output. 89 90:issue:`2609` 91:issue:`3094` 92 93Fix bug in gmx xpm2ps 94""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 95 96The tool would fail when not being provided with a library file to read in. 97 98:issue:`3012` 99 100Fix bug in gmx anaeig 101""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 102 103An issue was noted when reading a second set 104set of eigenvectors that could lead to problems when the number 105of eigenvectors was less than the three times the number of atoms. 106 107:issue:`2972` 108 109Fix issue with demux.pl script 110""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 111 112The trajectories could become discontinuous with simulations longer than 100ns 113and exchange strides that are not a multiple of 1 ps. This only affected the 114post-processing of trajectories generated from replica exchange simulations. 115 116Made gmx disre work with non-consecutively labeled restraints 117""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 118 119:issue:`2953` 120 121Fixed writing of gro files with index groups 122""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 123 124An output ``.gro`` file from from e.g. ``gmx editconf -f -n`` would 125take the atom names for the output file in order from the atoms in the 126input file, rather than in order from the atoms indicated by the 127indices in the index file. 128 129:issue:`3107` 130 131Made gmx make_ndx keep chain IDs 132""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 133 134Old style structure file reading caused the chain IDs to be overwritten with 135default values. 136 137:issue:`3070` 138 139Fixes that affect portability 140^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 141 142Disable PME OpenCL on Apple 143""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" 144 145The Apple OpenCL compilers fail to produce a functional clFFT build. 146The OpenCL PME support is therefore disabled on Apple platforms. 147 148:issue:`2941` 149 150Miscellaneous 151^^^^^^^^^^^^^ 152 153Added AMD Zen 2 detection 154^^^^^^^^^^^^^^^^^^^^^^^^^ 155 156The AMD Zen 2 architecture is now detected as different from Zen 1 157and uses 256-bit wide AVX2 SIMD instructions (GMX_SIMD=AVX2_256) by default. 158Also the non-bonded kernel parameters have been tuned for Zen 2. 159This has a significant impact on performance. 160