[gmx-users] molecule index
Justin A. Lemkul
jalemkul at vt.edu
Mon Sep 21 02:32:58 CEST 2009
Jamie Seyed wrote:
> Yes Thanks Justin, should I just use the linear part of msd for fit even
> if it is short (like 14ps from 200ps)? Thanks/Jamie
>
Yes, the linear portion of the graph should be used for MSD analysis. 200 ps is
somewhat short, but might be sufficient for water.
-Justin
> On Sun, Sep 20, 2009 at 8:02 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Jamie Seyed wrote:
>
> 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?
>
>
> Probably inadequate sampling, either from the number of frames
> saved, or from the length of the simulation itself.
>
> -Justin
>
> Thanks in Advance/Jamie
>
>
> On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto: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>
> <mailto:Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>
> <mailto: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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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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