[gmx-users] How to simulate broken and movement of molecules

[Anton Feenstra]

Albert Sun wrote:
> Thanks, Anton and users,
>  
> I understand this should reply on time scale and size, also forces applied, but
> I tried a few examples and could not see how those atoms are broken and separated.

You can try e.g. g_rdf to get an overall picture of molecule packings,
or you could inspect 'visually' using a trajectory viewer (e.g. ngmx or
vmd), or look at snapshots (e.g. load a pdb file in rasmol).

By the way, atoms are not likely to break... Also, molecules will not
break in MD, but they may separate... ;-)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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