NAMD 2.9b1 released

From: Jim Phillips (
Date: Tue Mar 20 2012 - 20:35:59 CDT

Dear NAMD users,

NAMD 2.9b1 is available for download (since yesterday with no bug reports
so far), with many new features noted below. This is a beta release, so
please test your simulations over the next few weeks and let us know of
any issues. I am hoping for a short beta cycle with minimal new code (and
much new documentation) added before the final 2.9 release.

Thank you all for your efforts and support.


| |
| NAMD 2.9b1 Release Announcement |
| |

                                                        March 19, 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 2.9b1 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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