[gmx-users] molecule index
Jamie Seyed
jamie.seyed at gmail.com
Mon Sep 21 02:29:43 CEST 2009
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
On Sun, Sep 20, 2009 at 8:02 PM, Justin A. Lemkul <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>> 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>>> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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