[gmx-users] molecule index

[Mark Abraham]

Jamie Seyed wrote:
> 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"

OK so apparently it wants atom indices for whole molecules. That seems 
much more plausible to me than David's advice you quoted (please give 
URLs to such quotes in future, perhaps you took it out of context...)

So try giving it atom indices for a whole water molecule as an 
experiment. Seems like an obvious try to me :-) Then, scale it up if it 
seems to work.

> I also did not understand what you pointed out about "One of these sets 
> of numbers is larger than the other" ...

One of the set of atom indices in a protein and the set of molecule 
indices in a solvated protein will have more members than the other. 
Instead of asking which is right, you might try out a case that will 
fail under one assumption and work under the other :-) Then perhaps ask 
a question with some evidence behind it.

> questions:
> 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 file??

Provide links, please. We're not going to duplicate your googling.

Mark

> 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 
> <mailto: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
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php