NAMD 2.12b1 released

From: Jim Phillips (
Date: Thu Nov 03 2016 - 17:06:48 CDT

Dear NAMD users,

NAMD 2.12b1 is available for download. This release includes new kernels
for both NVIDIA GPUs and Intel Xeon Phi Knight's Landing (KNL) processors
(not co-processor accelerators) along with a variety of performance,
scaling, and feature improvements. If there are issues the old GPU
kernels can be selected with "useCUDA2 no" and "usePMECUDA no", and
multi-threaded optimizations disabled with "useCkLoop 0". For details
please see

Please note that there is a change in the adaptive biasing force (ABF)
system force conventions in the collective variables module. For details

I am hoping for a short beta cycle with limited new code (and some new
documentation) added before the final 2.12 release in December.

Thank you all for your efforts and support.


| |
| NAMD 2.12b1 Release Announcement |
| |

                                                      November 2, 2016

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 2.12b1 has many advantages over NAMD 2.11, among these are:

- GPU-accelerated simulations up to three times as fast as NAMD 2.11

- Improved vectorization and new kernels for Xeon Phi Knight's Landing

- Improved scaling for large implicit solvent simulations

- Improved scaling for multi-threaded "smp" builds

- Communication thread sleeps in single-process-per-replica smp runs

- Divide GPUs among replicas on host with "+devicesperreplica n"

- Shared-memory parallel calculation of collective variables

- Tcl scripting of collective variables thermodynamic integration

- Constraints on probability distributions of collective variables

- Collective variables module improvements including to histogram bias

- Extended adaptive biasing force on-the-fly free energy estimator

- Dynamic lambda scaling for alchemical work calculations

- Scaling of bonded terms in alchemical free energy calculations

- Properly scaled alchemical Lennard-Jones long-range corrections

- Multigrator pressure and temperature control method

- Retry after spurious EXDEV (Invalid cross-device link) output errors

- Ability to modify grid force scaling without restarting

- Ability to reload molecular structure without restarting

- Optional Python scripting interface

- QM/MM simulation via interfaces to ORCA and MOPAC

- Update to Charm++ 6.7.1

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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