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NAMD 2.12 Announcement

December 22, 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 2.12 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 http://www.ks.uiuc.edu/Research/namd/2.12/features.html

NAMD is available from http://www.ks.uiuc.edu/Research/namd/

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 http://www.ks.uiuc.edu/Research/namd/performance.html

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 namd@ks.uiuc.edu.

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