[gmx-users] calculating dihedral properties

Anna MARABOTTI amarabotti at unisa.it
Wed Sep 25 18:08:15 CEST 2013


Dear all, 

I would like to calculate how three dihedrals in my
protein are evolving during the simulation time, but I don't understand
which is the correct command to do. 

In particular, I would like to

- what is the value of a specified dihedral (in degrees) 

- if
this value changes during the time of simulation 

- what is the
probability distribution of this angle. 

In order to answer to these
questions, first, I created an index file with make_ndx, in which I set
the three dihedrals of my interest by selecting the atoms of the
dihedrals. Then I used the command G_ANGLE -F PROT.XTC -N PROT.NDX -TYPE

Then, I
had a look at the results, but I really don't understand them...in any
case, they are not what I was expected to find. I was expecting to find
somewhere a graph in which on the X axis I have the time, and on the Y
axis the oscillation of the angle around an average value, expressed in
degrees. Moreover, I was expecting to create a graph with a
Gaussian-like shape, indicating what is the most frequent value assumed
by this dihedral during my simulation. None of the resulting graphs
appear like that. 

Finally, I used g_sgangle in order to understand if,
during the simulation, the distance and the angle between two aromatic
residues varies during the time. In the case of the angle variation, the
values on the Y axis of the resulting graph vary in all cases between -1
and 1. On the Y axis the legend states "Angle(degrees)" but it seems
very strange to me that all my dihedrals are set on this very narrow
range of values. 

Could you please help me? 

Many thanks and best


Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano
Phone: +39 089 969583
Fax: +39 089 969603
amarabotti at unisa.it
Skype: annam1972
Web page:

"Indifference is the
eighth deadly sin" (don Andrea Gallo)

More information about the gromacs.org_gmx-users mailing list