[gmx-users] molecule index

[Jamie Seyed]

Thanks Mark,
here are the links.
http://www.psc.edu/general/software/packages/gromacs/online/water.html

http://www.mail-archive.com/gmx-users@gromacs.org/msg07653.html

I tried your advice with 1 water molecule and since it worked I tried it
with SOL.ndx, but I got
D[SOL] -0.0333(+/- 0.0370) 1e-5 cm^2/s
It seems not reasonable to me (negative and its error is bigger than
itself). Any idea?
Thanks in Advance/Jamie

On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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
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