[gmx-users] g_angle for calculating dihedrals

[David van der Spoel]

Amit Choubey wrote:
> Hi everyone,
> 
> I was looking at calculation od dihedrals using g_angle. I did not 
> understand what the output of this tool is, along the x-axis we have 
> angle (in degrees) but what do we have along the y axis . Does y-axis 
> show the fraction of dihedrals having that specific angle? It does seem 
> so by adding all the fractions but i need to make sure.
> 
> Just to be sure that you know what i am talking about i first used 
> make_ndx to make a group of 4 atoms (whose dihedral has to be 
> calculated) . Then i used
> 
> g_angle -f confout.gro -n index.ndx -type dihedral
> 
> where index.ndx has the indices for all the relevant atoms stored in a 
> group.
> 
> Thank you,
> 
> Amit
> 
This is correct. You can also use mk_angndx for selecting specific 
dihedrals from your tpr file.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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