[gmx-users] make_ndx problem

[Justin A. Lemkul]

minnale wrote:
>   Thanks for the reply, may be this is trivial question to you
> That I know that how to select phosrous atom alone of POPC.
> Normally people are using only phosphrous atom or PO4 group ? for 
> density calculation ,etc analysis. In one article I found that they have 
> done density analysis for PO4 group.
> Could you please tell me which one use it for analysis if PO4 how select 
> by using make_ndx?
> Thanks alot in advance.

I have seen both P and PO4 analyzed, as well.  It's up to you to decide what is 
most relevant for your situation.

I updated the wiki page this morning to include some examples:

http://wiki.gromacs.org/index.php/make_ndx

-Justin

> 
> 
> On Wed, 16 Jul 2008 Florian Haberl wrote :
>  >Hi,
>  >
>  >On Wednesday, 16. July 2008, minnale wrote:
>  > > Hi Users,
>  > >  I want to do analysis of g_density of lipidbilayer so how can I 
> select po4
>  > > and N(CH3)3 groups seperately by using make_ndx from popc. Can 
> anyone tell
>  > > me detail with which options use?
>  > > I have checked in archives that create sn1.ndx and sn2.ndx files but i
>  > > didnt get celarly. Thanks in advance
>  >
>  >Take first a look on your .gro file and identify the atoms you want to 
> select.
>  >
>  >try something like:
>  >
>  >make_ndx -f your_file.gro
>  >
>  >a P*
>  >
>  >this should select all atoms with P in your system., it also depends 
> on the
>  >used force field.
>  >
>  >Also "h" prints out some inforamation about the selection choices.
>  >
>  >
>  >greetings,
>  >
>  >Florian
>  >
>  >--
>  >-------------------------------------------------------------------------------
>  >  Florian Haberl
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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