[gmx-users] molecule index

Mark Abraham Mark.Abraham at anu.edu.au
Sun Sep 20 21:33:18 CEST 2009

Jamie Seyed wrote:
> Dear all,
> I want to calculate the msd using g_msd. I have a macromolecule and some 
> (let say 100) water molecules and I want to use msd for water only. from 
> the manual and list I think I need to make an index for molecules 
> (water) and use -mol option.
>  From David's answer on the list I found
> -----------------------------------------------------
> "If you know which molecules they are then you just write in a text editor:
> [ mymolecules ]
> 3 5 19 23 45 109"
> ----------------------------------------------------
> My question is: let say the macromolecule is coming first in the pdb 
> file and then there are water molecules. If I want to make an index for 
> only waters, according to this advice, should I write 2 3 4... 100  
> (just remove 1 that goes for macromolecule)
> I am wondering if there is a confliction between these numbers(refer to 
> molecules) and atom numbers of macromolecule.... Would you please 
> clarify this for me??

Try it and see. One of these sets of numbers is larger than the other, 
and if you use a number in that interval you'll either get an error or 
success, either of which will answer your question.


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