[gmx-users] Where are the good tutorials?

[Tsjerk Wassenaar]

Casey,

Could you expand your criticism? You must have found the tutorials section
on the wiki. Then please note the specific points you dislike about the
tutorials there (especially the beginners) and provide some ideas you would
think improve them.

To my opinion, a beginners tutorial provides a set of standard parameters,
which will do for most of the simulations most of the users will encounter.
There is not much benefit in writing such a file from scratch, although one
should introduce the file and explain, also pointing to the file format. But
then, if you have a .pdb file and parameters, md simulations are little more
than 'punch in some commands', on top of the thinking about the process that
is effected by that.

I forgive students who feel that they don't need to go beyond punching the
commands to get the credits. But for someone like you, searching for a
tutorial to get into MD, I would think that the commands and the surrounding
text would be sufficient to keep you from only punching them in and obtain
the output. It will by all means be sufficient for someone interested to
extract the insights needed for getting started with MD. If you really want
to go beyond that (but that's not tutorial work), you'll find the Gromacs
documentation, explaining topologies and parameters in detail.

Cheers,

Tsjerk


On Thu, May 14, 2009 at 12:24 AM, Joseph Johnson <helstreak at hotmail.com>wrote:

>  Are there any good tutorials that start from the very beginning, like
> assuming you only have a .pdb file?  It seems that most of the tutorials
> I've found have already generated the files you need and then all you have
> to do is punch in some commands.  Where can I learn to actually write the
> molecular dynamics input file and all that good stuff?
>
> Thanks for your time and help,
> Casey
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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