[gmx-users] make_ndx problem

minnale minnale_gnos at rediffmail.com
Wed Jul 16 15:14:29 CEST 2008

  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. 

On Wed, 16 Jul 2008 Florian Haberl wrote :
>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.
>  Florian Haberl
>  Computer-Chemie-Centrum
>  Universitaet Erlangen/ Nuernberg
>  Naegelsbachstr 25
>  D-91052 Erlangen
>  Telephone:  	+49(0) − 9131 − 85 26573
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
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