NAMD 2.9 New Features

The following features have been released in NAMD 2.9. Any bug fixes will appear in the nightly build version on the download site. Any documentation updates will appear in the Nightly Build User's Guide (online or 5.0M PDF) and release notes.

Improved (temperature/Hamiltonian) replica-exchange implementation

Replica-based umbrella sampling via collective variables module

Optimized shared-memory single-node and multiple-node CUDA builds

CUDA GPU-accelerated generalized Born implicit solvent (GBIS) model

CUDA GPU-accelerated energy evaluation and minimization

Native CRAY XE/XK uGNI network layer implementation

Faster grid forces and lower-accuracy "lite" implementation

Hybrid MD with knowledge-based Go forces to drive folding

Linear combination of pairwise overlaps (LCPO) SASA for GBIS model

Weeks-Chandler-Anderson decomposition for alchemical FEP simulations

Collective variables module improvements

Updates to CUDA 4.0 and Tcl 8.5.9, plus option to build with FFTW 3