NAMD 2.9b2 released

From: Jim Phillips (
Date: Tue Mar 27 2012 - 15:17:30 CDT

Dear NAMD Users,

NAMD 2.9b2 is available for download (since yesterday with no bug reports
so far). This release incorporates collective variables updates including
the new dihedralPC component and a new metadynamics multiple replicas
implementation. For implicit solvent the LCPO option has been renamed
SASA and disabled by default for consistency with NAMD 2.8. I am hoping
for this to be the final beta release, so please test your simulations
over the next few weeks and let us know of any issues.

Thank you all for your efforts and support.


| |
| NAMD 2.9b2 Release Announcement |
| |

                                                         March 26, 2012

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 2.9b2 has many advantages over NAMD 2.8, among these are:

- 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

- Enhanced performance and scalability

Details at

NAMD is available from

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

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

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

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