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Bug #811

tutorials

Added by Anonymous almost 8 years ago. Updated over 6 years ago.

Status:
Closed
Priority:
Low
Assignee:
-
Category:
documentation
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Problems with tutorials in GROMACS 4.5.4

There is an extra pd-temp parameter in all the grompp.mdp files

The online documentation tells you to use the ngmx trajectory viewer but that one is not default included with GROMACS 4.5.4 (so maybe adding some text about installing ngmx would be helpful)

In the mixed tutorial the topol.top file includes
#include "methanol.itp"
but methanol.itp is not included in GROMACS 4.5.4 (but is included in the methanol tutorial) so
#include "../methanol/methanol.itp"
will work

also in the mixed tutorial
g_density -n index -o dens0 -b 0 -e 50 -d X
command is missing the -ng 2 (so that you can select x2 groups)

The speptide tutorial also has quite a few inconsistencies.

Sadly a new/updated version of the tutorials and online getting started guide might be needed.

Associated revisions

Revision 69facd71 (diff)
Added by Roland Schulz almost 7 years ago

Remove share/tutor

Not up-to-date and better tutorials exists.

Fixes #811

Change-Id: I52708a534e641039ccb05538e0a5387079370761

History

#1 Updated by Mark Abraham almost 8 years ago

To which tutorials are you referring?

#2 Updated by Anonymous almost 8 years ago

They are under “Getting Started” in the online manual http://manual.gromacs.org/
And the tutorial files are provided with gromacs in the folder gromacs/share/gromacs/tutor
Maybe these where meant to be discontinued?

#3 Updated by Justin Lemkul almost 8 years ago

Helgi Ingolfsson wrote:

They are under “Getting Started” in the online manual http://manual.gromacs.org/
And the tutorial files are provided with gromacs in the folder gromacs/share/gromacs/tutor
Maybe these where meant to be discontinued?

The tutorials are somewhat outdated. Significantly better tutorial material exists on the Tutorials page on gromacs.org. The provided material may be updated, but I've never seen anyone raise the issues you have, indicating that likely very few people use them.

#4 Updated by Roland Schulz almost 7 years ago

Since it is outdated and better exists, should we simply remove it and replace it with a README containing a link to http://www.gromacs.org/Documentation/Tutorials ?

#5 Updated by Justin Lemkul almost 7 years ago

Roland Schulz wrote:

Since it is outdated and better exists, should we simply remove it and replace it with a README containing a link to http://www.gromacs.org/Documentation/Tutorials ?

That could be a good idea. I suppose if anything changed about the organization of www.gromacs.org, then we could make this corresponding change, as well.

#6 Updated by Teemu Murtola over 6 years ago

  • Category set to documentation
  • Status changed from New to Closed
  • Target version set to 4.6

Closing, since the mentioned tutorials have been removed.

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