[gmx-developers] mtop structure

[Anton Feenstra]

Alexander Malafeev wrote:
> I am uderstand how to use fields in this structure and what it means, 
> but I am not understand how to initialize and read this structure from 
> trajectory.

Not sure if I understand you well, but it seems you may be a bit 
off-track here.

As Mark explained, mtop holds your molecules, as per the [ molecules ] 
section in the topology file.

Therefore, it is not stored in the trajectory (that holds only the 
coordinates), but in the topology file. There are a number of topology 
reading routines in the library, which also get used by many analysis 
tools. Check for one that has a tpr file as obligatory input (ngmx 
springs to mind), and see how that code works.


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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