Re: NAMD 2.11b1 released

From: Tristan Croll (
Date: Wed Nov 11 2015 - 20:11:00 CST

Hi Jim,

A doubling of CUDA performance is very exciting! Are the best speed-ups seen in smaller or larger systems?



From: <> on behalf of Jim Phillips <>
Sent: Wednesday, 11 November 2015 1:39 AM
Subject: namd-l: NAMD 2.11b1 released

Dear NAMD users,

NAMD 2.11b1 is available for download (since last night), 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 limited new code (and some new
documentation) added before the final 2.11 release.

Thank you all for your efforts and support.


| |
| NAMD 2.11b1 Release Announcement |
| |

                                                     November 10, 2015

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 2.11 has many advantages over NAMD 2.10, among these are:

- GPU-accelerated simulations up to twice as fast as NAMD 2.10

- Enhanced Tcl scripting of collective variables and "cv" command

- Collective variables module improvements including to histogram bias

- TclForces query total net forces for atom groups

- Replica-exchange multiplexing (fewer partitions than replicas)

- Tcl scripting multiple in-memory checkpoints

- Improved Tcl scripting multi-copy interface documentation

- Tcl scripting asynchronous multi-copy remote in-memory checkpoints

- Tcl scripting asynchronous multi-copy remote trajectory output

- Tcl scripting asynchronous multi-copy remote script evaluation

- Tcl scripting asynchronous multi-copy central work queue support

- Tcl scripting asynchronous multi-copy workflow-style programming

- Improved minimization for Drude force field and rigid bonds

- Improved long-range LJ correction with VDW force switching

- Improved alchemical calculations with VDW force switching

- Pressure calculation with fixed atoms on GPU works as on CPU

- Improved scaling for GPU-accelerated particle-mesh Ewald calculation

- Improved scaling for GPU-accelerated simulations

- Improved scaling for multi-threaded "smp" builds

- Prevent running smp builds with one thread per process

- Support trajectory files larger than 2GB on Windows

- Improved Intel Xeon Phi coprocessor support

- Update to Charm++ 6.7.0 with improved multi-copy support

- Ignore ioformat statement in CHARMM topology and parameter files

- Psfgen improvements including long resids and insertion codes

- Psfgen package available in NAMD Tcl interpreter

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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