<P>
Thanks for the reply, may be this is trivial question to you<BR>
That I know that how to select phosrous atom alone of POPC.<BR>
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.<BR>
Could you please tell me which one use it for analysis if PO4 how select by using make_ndx?<BR>
Thanks alot in advance. <BR>
<BR>
<BR>
On Wed, 16 Jul 2008 Florian Haberl wrote :<BR>
>Hi,<BR>
><BR>
>On Wednesday, 16. July 2008, minnale wrote:<BR>
> > Hi Users,<BR>
> > I want to do analysis of g_density of lipidbilayer so how can I select po4<BR>
> > and N(CH3)3 groups seperately by using make_ndx from popc. Can anyone tell<BR>
> > me detail with which options use?<BR>
> > I have checked in archives that create sn1.ndx and sn2.ndx files but i<BR>
> > didnt get celarly. Thanks in advance<BR>
><BR>
>Take first a look on your .gro file and identify the atoms you want to select.<BR>
><BR>
>try something like:<BR>
><BR>
>make_ndx -f your_file.gro<BR>
><BR>
>a P*<BR>
><BR>
>this should select all atoms with P in your system., it also depends on the<BR>
>used force field.<BR>
><BR>
>Also "h" prints out some inforamation about the selection choices.<BR>
><BR>
><BR>
>greetings,<BR>
><BR>
>Florian<BR>
><BR>
>--<BR>
>-------------------------------------------------------------------------------<BR>
> Florian Haberl<BR>
> Computer-Chemie-Centrum<BR>
> Universitaet Erlangen/ Nuernberg<BR>
> Naegelsbachstr 25<BR>
> D-91052 Erlangen<BR>
> Telephone: +49(0) − 9131 − 85 26573<BR>
> Mailto: florian.haberl AT chemie.uni-erlangen.de<BR>
>-------------------------------------------------------------------------------<BR>
</P>
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