Ready for Testing

The following features will be released in NAMD 2.13, but are available now in the nightly build version on the download site. These features are documented in the Nightly Build User's Guide (online or 1.8M PDF) and release notes.

GPU-accelerated simulations less limited by CPU performance

Contributed by Antti-Pekka Hynninen. Bonded forces and exclusions are now offloaded to the GPU by default. (May be disabled with "bondedCUDA 0". Note that this is a bit flag so default is "bondedCUDA 255"; setting "bondedCUDA 1" will offload only bonds, not angles, dihedrals, etc.) Removes all load-balanced work from the CPU, leaving only integration and optional features. The only benefit is for machines that were limited by CPU performance, so a high-end dual-socket workstation with an older GPU may see no benefit, while a single-socket desktop with the latest 1080 Ti will see the most.

Improved GPU-accelerated performance for non-orthogonal cells

The "useCUDA2" and "usePMECUDA" kernels introduced in NAMD 2.12 now also support non-orthogonal periodic cells.

Gaussian accelerated MD (GaMD)

Contributed by Andrew Pang and Yi Wang.

Collective variables module improvements

Contributed by Giacomo Fiorin and Jerome Henin.

IMDignoreForces option for QwikMD

Blocks steering forces while still allowing pause/resume/exit commands.

Various psfgen improvements

When reading topology files, recognize READ statements even if previous END statement is missing, and warn and ignore on self and duplicate bonds. For topology file PRES (patch) entries support ATOM record with name but no type or charge to specify subsequent atom insertion order. Extend segment command to query charge.

Preliminary support for billion-atom systems

Fixed 32-bit integer overflows in psfgen, structure compression (takes 2 hours), and memopt build. Minimally tested on 10x10x10 grid of STMV with ldBalancer none.

Update to Charm++ 6.8.2

Various bug fixes and performance enhancements.

Require CUDA 8.0 or greater, Kepler or newer GPUs

Includes kernels compiled for Kepler, Maxwell, and Pascal GPUs. Support for Fermi GPUs was dropped in NAMD 2.12.