October 16, 2018

The Theoretical and Computational Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Institute of General Medical Sciences.

NAMD 2.13b2 has many advantages over NAMD 2.12, including:

- GPU-accelerated simulations less limited by CPU performance

- Improved GPU-accelerated performance for non-orthogonal cells

- Updated CUDA compatibility to version 9.x

- Replica exchange solute tempering, 2nd generation (REST2)

- Constant-pH MD

- Improvements to hybrid QM/MM simulation

- Stochastic velocity rescaling thermostat

- Gaussian accelerated MD (GaMD)

- Improved lonepair support

- Interleaved double-wide sampling for FEP

- Extend nonbondedScaling to LJ correction term

- Collective variables module improvements

- IMDignoreForces option for QwikMD

- Various psfgen improvements

- Support for billion-atom systems

- Update to Charm++ 6.8.2

- Require CUDA 8.0 or greater, Kepler or newer GPUs

Details at http://www.ks.uiuc.edu/Research/namd/2.13/features.html

NAMD is available from http://www.ks.uiuc.edu/Research/namd/

For your convenience, NAMD has been ported to and will be installed on the machines at the NSF-sponsored national supercomputing centers. If you are planning substantial simulation work of an academic nature you should apply for these resources. Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html

The Theoretical and Computational Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd@ks.uiuc.edu.

We are eager to hear from you, and thank you for using our software!