NAMD 2.7b3 released

From: Jim Phillips (
Date: Tue Jul 06 2010 - 13:45:58 CDT

Dear NAMD-L,

NAMD 2.7b3 may be downloaded from
and is installed in my home directories on Abe, Ranger, and Kraken. See for
specifics on those platforms and other updates. We're using the newly
released Charm++ 6.2.1 with mpiexec support for InfiniBand ibverbs job
launches and improved processor affinity options.

The SMP builds (installed at the centers but not available for download in
this release) are giving improved performance in a few cases, but mostly
allow larger systems to be run within available memory. Please try them
out! If there are no stability issues the SMP builds will become the
standard 2.7 downloads once performance and portablity is worked out.


| |
| NAMD 2.7b3 Release Announcement |
| |

                                                        July 6, 2010

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 Center for Research Resources.

NAMD 2.7b3 has many advantages over NAMD 2.6, among these are:

- Collective variable-based calculations

- Improved free energy methods for alchemical transformations

- Grid-based forces and molecular dynamics flexible fitting

- Additional bonded terms for restraining molecular structure

- Support for TIP4P water model

- Support for CHARMM Drude polarizable force field

- Support for C2 long-range electrostatics splitting function

- Support for VDW force switching and long-range tail corrections

- NVIDIA CUDA GPU acceleration of nonbonded force evaluation

- Direct (non-MPI) support for InfiniBand via OFED ibverbs library

- Use of mpirun to launch non-MPI (network or ibverbs) binaries

- 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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