[gmx-users] g_angle for calculating dihedrals

David van der Spoel spoel at xray.bmc.uu.se
Sat Nov 28 09:56:08 CET 2009

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 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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