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.

Issue 2047 Issue 2049

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 (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.

Issue 2046 Issue 2050

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.

Issue 2013

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.

Issue 1941

Fixed Parrinello-Rahman with nstpcouple > 1

Issue 2031

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.

Issue 2040

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.

Issue 2007

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.

Issue 2022