June 14, 2024

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 through grant numbers NIH P41-GM104601 and NIH R24-GM145965.

NAMD 3.0 has many advantages over NAMD 2.14, including:

- GPU-resident mode providing very fast dynamics:

   - Achieves 2x or more speedup on single GPU versus GPU-offload mode, and 7x or more speedup for multi-GPU scaling on NVIDIA DGX-A100 versus GPU-offload mode

   - Supports single GPU and single-node multi-GPU scaling for tightly coupled GPUs (e.g. NVLink-enabled architectures like DGX)

   - Improved performance for small systems (e.g., 23.6k atom DHFR benchmark using hydrogen mass repartitioning with AMBER force field parameters can achieve over 1 microsecond/day simulation rates on NVIDIA A100)

   - Supports essential dynamics simulation protocols: constant energy, thermostats, barostats, rigid bond constraints, multiple time stepping, PME

   - Supports standard TIP3P and advanced 4-site water models (TIP4P and OPC)

   - Supports minimize and run directives through TCL scripting

   - Supports several advanced features: replica-exchange MD, alchemical free energy methods (FEP & TI), REST2, harmonic restraints, external electric field, SMD, Colvars, TCL forces, Monte Carlo barostat, group position restraints, constant pH MD

- GPU-accelerated alchemical free energy methods (FEP & TI) for both GPU-offload and GPU-resident modes

   - Supports van der Waals force switching for alchemy on both GPU modes

- HIP kernel improvements for better performance on AMD GPUs

- CPU-vectorization mode compatible with Intel and AMD CPU models that support AVX-512 instructions

   - Achieves speedup of up to 1.8x on Intel Xeon over AVX2 builds

   - Exhibits good scaling on TACC Frontera supercomputer

- Extend REST2 force field compatibility

- Update Colvars to version 2024-06-04

- Update user guide documentation for GPU-resident mode

- Fix several long-standing issues

   - Fix CPU memory leaks

   - Fix race conditions running GPU-resident mode with Colvars or TCL forces

   - Fix GPU-resident mode running constant pressure with harmonic restraints

   - Fix race conditions and NaNs running alchemy on GPU

   - Fix using advanced features together with GPU atom migration

   - Implement moving averages for GPU-resident reduction averages

   - Update config file parameters to use "GPU" rather than "CUDA" naming

   - Improve guard against running GPU-resident with unsupported features

- Update Psfgen to version 2.0

   - Fix compatibility with constant-pH MD

- Update to TCL version 8.6.13 for GPU-resident with Colvars and TCL forces

- Update to Charm++ 8.0.0, enabling:

   - Updated implementation of atomics, locks, and fences to use C++11/C11 versions where suitable

   - Improved performance, support, and fixes for UCX

   - Improved scaling on InfiniBand via ucx network layer

   - Improved multi-copy on POWER via pamilrts network layer

   - Clean exit with non-zero status for many failures

   - Improved scaling on HPE/Cray Slingshot 11 via ofi network layer

- Support for CUDA versions 9.1-12.x on Maxwell or newer GPUs

- Support for compatible AMD GPUs via HIP

Details at http://www.ks.uiuc.edu/Research/namd/3.0/features.html

Benchmarks at https://www.ks.uiuc.edu/Research/namd/benchmarks/

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!