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
[email protected] [email protected] http://folding.bmc.uu.se
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