[gmx-users] g_sorient

David spoel at xray.bmc.uu.se
Sun Jul 6 22:37:01 CEST 2003


On Sun, 2003-07-06 at 17:45, Kay Gottschalk wrote:
> Hi there,
> 
> I want to use g_sorient to describe the orientation of 2 different 
> subsets of water around my protein. I am not quite clear how the index 
> file has to look like; do I have to use an index file with molecule 
> numbers (as for g_msd), or with the atom number of the oxygen or with 
> all atom numbers of the water molecules considered?
I don't think you need an index file. Have you tries just playing with
the distances?


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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