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Bug#252101: marked as done (ITP: gromacs -- versatile package to perform molecular dynamics [med-bio])

Your message dated Sun, 26 Mar 2006 09:14:36 -0800
with message-id <E1FNYp2-0006W4-Sc@spohr.debian.org>
and subject line Bug#252101: fixed in gromacs 3.3-1
has caused the attached Bug report to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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Debian bug tracking system administrator
(administrator, Debian Bugs database)
--- Begin Message --- 
Package: wnpp
Severity: wishlist

* Package name    : gromacs
  Version         : 3.2.1
  Upstream Author : David van der Spoel <spoel@gromacs.org>, Berk Hess <hess@gromacs.org>, Erik Lindahl <lindahl@gromacs.org>
* URL             : http://www.gromacs.org/
* License         : GPL
  Description     : [Biology] versatile package to perform molecular dynamics

 GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
 It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
 GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition:
 .
 GROMACS provides extremely high performance compared to all other programs. A lot of algorithmic optimizations have been introduced in the code; we have for instance extracted the calculation of the virial from the innermost loops over pairwise interactions, and we use our own software routines to calculate the inverse square root. The innermost loops are generated automatically in either C or Fortran at compile time, with optimizations adopted to your architecture. Assembly loops using SSE and 3DNow! multimedia instructions are provided for x86 processors, resulting in exceptional performance on inexpensive PC workstations. For Pentium IV processors there are even SSE2 double precision assembly loops, and on Power PC G4 and later processors we provide Altivec loops both for Linux and Mac OS X. Gromacs is normally 3-10 timesfaster than any other program; check the article in Journal of Molecular Modeling (reference can be found under resources) for a comparison benchmark.
 .
 GROMACS is user-friendly, with topologies and parameter files written in clear text format. There is a lot of consistency checking, and clear error messages are issued when something is wrong. Since the C preprocessor is used, you can have conditional parts in your topologies and include other files. You can even compress most files and GROMACS will automatically pipe them through gzip upon reading.
 .
 There is no scripting language - all programs use a simple interface with command line options for input and output files. You can always get help on the options by using the -h option, or use the extensive manuals provided free of charge in electronic or paper format. There is also an integrated graphical user interface available for all programs.
 .
 As the simulation is proceeding, GROMACS will continuously tell you how far it has come, and what time and date it expects to be finished.
 .
 Both run input files and trajectories are independent of hardware endian and can thus be read by any version GROMACS, even if it was compiled using a different floating-point precision. All files from GROMACS 2.0 can further be used in the new version 3!
 .
 GROMACS can write coordinates using lossy compression, which provides a very compact way of storing trajectory data. The accuracy can be selected by the user.
 .
 GROMACS comes with a large selection of flexible tools for trajectory analysis - you won't have to write any code to perform routine analyses. The output is further provided in the form of finished Xmgr/Grace graphs, with axis labels, legends, etc. already in place!
 .
 A basic trajectory viewer that only requires standard X libraries is included, and several external visualization tools can read the GROMACS file formats.
 .
 GROMACS can be run in parallel, using standard MPI communication.
 .
 GROMACS contains several state-of-the-art algorithms that make it possible to extend the time steps is simulations significantly, and thereby further enhance performance without sacrificing accuracy or detail.
 .
 The package includes a fully automated topology builder for proteins, even multimeric structures. Building blocks are available for the 20 standard aminoacid residues as well as some modified ones, the 4 nucleotide and 4 deoxinucleotide resides, several sugars and lipids, and some special groups like hemes and several small molecules.
 .
  Homepage: http://www.gromacs.org/
 
A first package is soon available under
http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/gromacs

If one of the readers of debian-devel would fancy to sponsor this
package then I'd very much appreciate it.

Steffen


-- System Information:
Debian Release: testing/unstable
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: i386 (i686)
Kernel: Linux 2.4.20
Locale: LANG=de_DE, LC_CTYPE=de_DE

--- End Message ---
--- Begin Message --- 
Source: gromacs
Source-Version: 3.3-1

We believe that the bug you reported is fixed in the latest version of
gromacs, which is due to be installed in the Debian FTP archive:

gromacs-dev_3.3-1_i386.deb
  to pool/main/g/gromacs/gromacs-dev_3.3-1_i386.deb
gromacs-doc_3.3-1_all.deb
  to pool/main/g/gromacs/gromacs-doc_3.3-1_all.deb
gromacs-lam_3.3-1_i386.deb
  to pool/main/g/gromacs/gromacs-lam_3.3-1_i386.deb
gromacs-mpich_3.3-1_i386.deb
  to pool/main/g/gromacs/gromacs-mpich_3.3-1_i386.deb
gromacs_3.3-1.diff.gz
  to pool/main/g/gromacs/gromacs_3.3-1.diff.gz
gromacs_3.3-1.dsc
  to pool/main/g/gromacs/gromacs_3.3-1.dsc
gromacs_3.3-1_i386.deb
  to pool/main/g/gromacs/gromacs_3.3-1_i386.deb
gromacs_3.3.orig.tar.gz
  to pool/main/g/gromacs/gromacs_3.3.orig.tar.gz



A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 252101@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Nicholas Breen <nbreen@ofb.net> (supplier of updated gromacs package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.7
Date: Thu, 16 Mar 2006 23:00:13 -0800
Source: gromacs
Binary: gromacs gromacs-lam gromacs-dev gromacs-mpich gromacs-doc
Architecture: source i386 all
Version: 3.3-1
Distribution: unstable
Urgency: low
Maintainer: Nicholas Breen <nbreen@ofb.net>
Changed-By: Nicholas Breen <nbreen@ofb.net>
Description: 
 gromacs    - Molecular dynamics simulator, with building and analysis tools
 gromacs-dev - GROMACS molecular dynamics sim, development kit
 gromacs-doc - GROMACS molecular dynamics sim, documentation
 gromacs-lam - Molecular dynamics sim, binaries for LAM-MPI parallelization
 gromacs-mpich - Molecular dynamics sim, binaries for MPICH parallelization
Closes: 228319 252101
Changes: 
 gromacs (3.3-1) unstable; urgency=low
 .
   * Initial Debian release.  (Closes: #228319, #252101)
Files: 
 69ca4efac6260b371b2715d8e672db27 780 science extra gromacs_3.3-1.dsc
 99ea6f25a89f1511f51c350a66a2fdc4 5906342 science extra gromacs_3.3.orig.tar.gz
 57cb2f57b0e740c21746d36184386662 2204977 science extra gromacs_3.3-1.diff.gz
 5ad9bbb08805effc11f39d19787ce994 2542278 science extra gromacs-doc_3.3-1_all.deb
 1e68e05788cb8b5262c1bde79316e80f 3513716 science extra gromacs_3.3-1_i386.deb
 dabf269835a78a643b6e0349b26f0257 5377818 science extra gromacs-dev_3.3-1_i386.deb
 f57988ac58445fee2eecb527cf004e96 1558976 science extra gromacs-mpich_3.3-1_i386.deb
 be78981ba850b88d8595d66017ac1b22 1321990 science extra gromacs-lam_3.3-1_i386.deb

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