Re: NAMD 2.11 released

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Dec 23 2015 - 19:38:21 CST

LOL

On Wednesday, December 23, 2015, Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> A Win32 binary now appears in the download list. It's a Festivus miracle!
>
> Jim
>
>
> On Tue, 22 Dec 2015, Branko wrote:
>
> Jim,
>>
>> Thank you for announce. Since 2.10 versions all win binaries are for 64
>> bit machines. Sorry if question is not so clever, but is it possible that
>> (win) 32bit version appear among version offered for download. I know that
>> 32bit operative systems are outdated, still there are some users which like
>> XP and similar systems, and, as a rule, all calculation prepared for Linux
>> clusters initially 'try' on desktops. Thanks
>>
>> Branko
>>
>>
>>
>> On 12/22/2015 5:38 PM, Jim Phillips wrote:
>>
>>> Dear NAMD users,
>>>
>>> NAMD 2.11 is officially released and available for download.
>>>
>>> This release fixes a bug that resulted in incorrect VDW tail correction
>>> values for systems larger than about 11,000 atoms due to an integer
>>> overflow. This feature is off by default, and the magnitude of the
>>> incorrect energy and pressure correction factor was always smaller than the
>>> correct value and declined with increasing system size. Again, this bug
>>> only affected simulations with LJcorrection explicitly enabled.
>>>
>>> Thank you all for your efforts and support!
>>>
>>> Jim
>>>
>>>
>>> +--------------------------------------------------------------------+
>>> | |
>>> | NAMD 2.11 Release Announcement |
>>> | |
>>> +--------------------------------------------------------------------+
>>>
>>> December 22, 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
>>>
>>> - Fix long-range LJ correction for systems larger than 11,000 atoms
>>>
>>> - 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
>>>
>>> - NVIDIA CUDA GPU-acceleration binaries for Mac OS X
>>>
>>> - 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!
>>>
>>>
>>
>

-- 
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

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