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
> Computer-Chemie-Centrum
> Universitaet Erlangen/ Nuernberg
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> Telephone: +49(0) − 9131 − 85 26573
> Mailto: florian.haberl AT chemie.uni-erlangen.de
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
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