[gmx-users] Re: Targeted MD

[Mark Abraham]

Steven Kirk wrote:
> Mark Abraham <Mark.Abraham at anu.edu.au> wrote

>> "Non-Protein" serves well here. So a usual tc-grps line has "Protein 
>> Non-Protein" for a protein simulation.
>>
>> Mark
> 
> A supplementary question.
> 
> The tc-grps line can take predefined standard group names such as 
> 'System', 'Protein' and 'Non-Protein'.
> 
> Does the 'Protein' group need to actually BE a protein, or are 'Protein' 
> and 'Non-Protein' really synonyms for 
> 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ?

I haven't read the code or found any mention in the manual, but I expect 
that src/share/top/aminoacids.dat contains the names of any amino acids, 
and thus implicitly defines these groups.

Mark