[gmx-users] calculating dihedral properties

Justin Lemkul jalemkul at vt.edu
Wed Sep 25 19:43:10 CEST 2013

On 9/25/13 12:08 PM, Anna MARABOTTI wrote:
> 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
> know:
> - 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.

It would be helpful to see images of what you've got, but I suspect it all comes 
down to the fact that you're analyzing multiple dihedrals without using the -all 
option.  Per the second paragraph of g_angle -h:

"With option -ov, you can plot the average angle of a group of angles as a
function of time. With the -all option, the first graph is the average and
the rest are the individual angles."

The -od output should give you the distribution, but I can't envision what you 
got as output.

> 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.

I think that's a small output labeling bug.  If the range is {-1..1} then it's 
probably the cosine of the angle, not the angle itself, but IIRC the angle is 
listed in the second column of the .xvg file.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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