[gmx-users] molecule index

Jamie Seyed jamie.seyed at gmail.com
Mon Sep 21 00:55:12 CEST 2009

Hi Mark,
Thanks for the puzzling answer. I tried the index file counting the number
of water molecule but I got an error.
"Fatal error:
The index group does not consist of whole molecules"
I also did not understand what you pointed out about "One of these sets of
numbers is larger than the other" ...
1) for msd calculation for water molecules, do I need really make index file
for all waters,
2) What I made (count the water molecules in a [mymolecules] index file),
did not work. How I suppose to do make that?
3) In getting started-Water page that I found in google it only say "g_msd
-n index" and did not explain which index... how about if I use oxygen.ndx
I really appreciate your help. Many Thanks in Advance/Jamie

On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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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