From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Sun Dec 06 2015 - 22:01:09 CST
Dear NAMD users,
NAMD 2.11b2 is available for download (since Friday night), with new Mac
CUDA binaries and several bug fixes. This is hopefully the last beta
release before 2.11 final, so please test your simulations over the next
few weeks and let us know of any issues.
Thank you all for your efforts and support.
Jim
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| NAMD 2.11b2 Release Announcement |
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December 4, 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 http://www.ks.uiuc.edu/Research/namd/2.11/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_at_ks.uiuc.edu.
We are eager to hear from you, and thank you for using our software!
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