ANNOUNCE: NAMD 2.0 Release

David Lloyd-Jones icomm5 at netcom.ca
Mon Mar 29 22:38:03 EST 1999


My goodness, if this discussion group is devoted to advertising software we
might as well all go home.

One would have thought people would say what they were doing, and
incidentally perhaps what software they were using, as a way to saying what
they tought they might have found out.

Science is, after all, about findings, however tentative.

It is not about the advertising of tools.(*)

                                                      -dlj.

* I admit that something like 20% of all the Nobels have been given to
toolmakers for the making of tools. I hope, however, that you will take the
point of my criticism straight to your heart...

                                                                -d.


Jim Phillips <jim at ks.uiuc.edu> wrote in message
news:7dh0ef$nlo at net.bio.net...
> +--------------------------------------------------------------------+
> |                                                                    |
> |                   NAMD 2.0 Release Announcement                    |
> |                                                                    |
> +--------------------------------------------------------------------+
>
>                                                        March 25, 1999
>
> The Theoretical 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.  NAMD2 is a major
> improvement over NAMD 1.5, in both speed and simulation features.
>
> This is a binary-only release of NAMD2.  We still have some additional
> code cleanup before releasing the source in a couple of weeks.
>
> NAMD2 is available via the web at http://www.ks.uiuc.edu/Research/namd/.
> Mail any questions or comments to namd at ks.uiuc.edu.
>
> ----------------------------------------------------------------------
>
> New Features in NAMD 2.0
>
> - Reads CHARMM (or X-PLOR) formatted parameter files.
>
> - Supports periodic and non-periodic MD simulations.
>
> - Particle mesh Ewald full electrostatics for periodic simulations.
>
> - Triple timestepping.
>
> - Rigid bonds to hydrogen atoms.
>
> - Fixed atoms implemented efficiently, no unnecessary force
> calculations.
>
> - Berendsen and Langevin piston constant pressure methods.
>
> - Steered Molecular Dynamics (SMD) features.
>
> ----------------------------------------------------------------------
>
> Problems?
>
> For problems or questions, send email to namd at ks.uiuc.edu.  If you
> think you have found a bug, please include what machine you are
> running on, and, if possible, a dump of the program output and/or a
> copy of your input files.  Your feedback will help us improve NAMD2.
>
> ----------------------------------------------------------------------
>
> NAMD2 Known Deficiencies
>
> - PME does not parallelize well and has had limited testing.
>
> - NAMD2 requires X-PLOR or CHARMM to produce the .psf structure input
> files.  If you don't have one of these, you probably can't use NAMD2
> yet.
>
> ----------------------------------------------------------------------
>
>






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