[gmx-users] Spherical orientational distribution function

[David van der Spoel]

On Mon, 25 Mar 2002, Peter Fojan wrote:

>Hi all,
>can anybody give me a hint on how I can calculate the Spherical
>orientational distribution function from a dynamics simulation in
>Gromacs?
>I want to calculate the Spherical orientational distribution function
>for a sidechain of an aminoacid. The Calpha-Cbeta from an alanine in a
>protein.
Maybe g_rotacf can do it, but you must first make a "fitted" trajectory, 
i.e. use trjconv to make a new trajecotry ( of your protein only) that 
contains a protein lsq fitted on the starting structure.
g_rotacf -d with appropriate index file should do it.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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