Removed HIS1 from oplsaa and charmm definitions¶
HIS1 is intended for linking with heme, which oplsaa doesn’t define. charmm converts HIS1 to HSD in its .r2b.
This makes the recent fix for oplsaa HISD “consistent” with HIS1.
Fixed amber03 charges for HIP and LYN¶
LYN charges now match those found in AMBER 14 and 16. The validation of the ports of AMBER force fields to GROMACS was done with AMBER 8.0, and this fix was made afterwards in http://ambermd.org/bugfixes/8.0/bugfix.19 (and perhaps LYN wasn’t in the validation set).
HIP was changed in AMBER source in Nov 2005, and the charges now match AmberTools 16.
Fixed OPLS/AA-L charges for HISD and HISE¶
With the present charges, the results from Michael Shirts et al. J. Chem. Phys. 119 (2003) 5740 can be reproduced.
Fixed bug with conjugate-gradient and OpenMP¶
The conjugate-gradient update routine re-used the pointer variable for x for cg_p. This pointer was shared over threads and no barrier was present before the pointer modification.
Fixed Parrinello-Rahman with nstpcouple > 1¶
Fixed Ewald surface+3DC corrections¶
Ewald surface and 3DC correction forces were only applied up to, but not including, the last atom with exclusions. With water at the end of the system only the last H would not be corrected. With ions at the end all ions would be missing. In addition, with the Verlet scheme and domain decomposition no force correction was applied at all.
Fixed twin-ranged cutoff for potential-switch LJ running on GPUs¶
With rcoulomb > rvdw, as often used with PME tuning, the GPU kernels performed the LJ cut-off check before applying the potential switch to the LJ forces and energies.
Added work-around for glibc 2.23 with CUDA¶
This makes it straightforward to build GROMACS with e.g. Ubuntu 16.04 that ships gcc with this glibc that CUDA does not formally support.