[gmx-users] order parameters

[Graham Smith]

On Mon, 17 Jan 2000, Peter Fojan wrote:

> Hi all,
> does anyone have any suggestions on how I could extract the order
> parameters for an amino acid side chain from a dynamics trajectory done
> by gromcacs? Any help would be greatly appreciated
> Peter

Is g_chi what you want? It does order parameters for each dihedral angle
of each residue, eg just

g_chi -f prodn.xtc -c prodn.tpr -maxchi 2 
will produce order.xvg 

(though when I did a test, not all the chi2 order parameters look right
to me.. a lot of them are the same) 

add -all to get angle vs t of every dihedral of every residue. 
add -corr dihcor.xvg to get this and also a correlation function for every
dihedral of every residue. 
(if doing this, run the program in its own directory so you can easily
clean up the hundreds of output files!) 

(BTW There are other features, e.g calculating numbers of transitions
between rotamers, that seem not to be implemented yet - has anybody out
there been working on this? Because if not I'll try to fix it myself) 

-Graham 

########################################################################

Dr. Graham R. Smith, 
Biomolecular Modelling Laboratory, 
Imperial Cancer Research Fund, 
44 Lincoln's Inn Fields, 
London WC2A 3PX,
U.K. 
Tel: +44-(0)20 7269 3348 
email: graham.smith at icrf.icnet.uk
URL: http://www.bmm.icnet.uk/~smithgr

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