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.
Mark
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