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Re: Bug#252101: ITP: gromacs -- [Biology] versatile package to perform molecular dynamics.

Steffen Moeller <moeller@rack7.pzr.uni-rostock.de> wrote:

> 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

For my taste, this long description is much too long, and most of it
could be put into README. Just mention the key point with one word or
short sentence: 

>  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.

So far, it's o.k. (Although I'd write it differently)

>  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:

Leave out the part in parentheses, and you could as well just write
something like "...all common algorithms. Special features are:"

>  GROMACS provides extremely high performance

... and makes use of hardware optimization on x86 and PowerPC
platforms. It is capable of running in parallel, using MPI

>  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.

GROMACS has a menu-driven, interactive interface with clear error
message and a wizard-like consistency check of user input, and includes
online as well as comprehensive printable documentation.

>  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.

Other features are:

* can write coordinates with lossy compression of arbitrary accuracy

* contains analysis tools and viewers

* contains a topology builder (what's that, btw?)

> 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.

I'd be interested, I'll have a look at the package.

Regards, Frank

Frank Küster, Biozentrum der Univ. Basel
Abt. Biophysikalische Chemie

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