[gmx-users] make_ndx problem

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed Jul 16 14:24:38 CEST 2008


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                        
 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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