[gmx-users] rm_pbc

[Anton Feenstra]

Christoph Freudenberger wrote:
> hi there,
> 
> I have finished the first version ot the sdf tool.
> While "cleaning" the source code I noticed that the
> function rm_pbc uses a structure of type 't_topology'.
> Is it vital for the correct pbc handling that a
> topology has been read from a .tpr file?
> 
> The programm runs fine withot and appearently the output
> is the same, I just want to be sure.

rm_pbc makes molecules whole again. mdrun only writes whole
molecules, but one might want to analyze output from other
programs. In order for rm_pbc to know which atoms are bound
together in one molecule, it needs the topology.

In most analysis tools, the topology is now actually optional,
in which case the user should know if her molecules are whole.

By the way, 'cleaning' g_rdf was a good idea. I've done some
of the rough 'demolition'-type of cleaning some time ago, but
didn't have time nor incentive to do the tiny things.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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