[gmx-users] molecule index

Jamie Seyed jamie.seyed at gmail.com
Sun Sep 20 19:06:18 CEST 2009

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??
Many Thanks in advance/Jamie
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