[gmx-users] Re: Re: calculating dihedral properties

Anna Marabotti amarabotti at unisa.it
Fri Sep 27 14:18:08 CEST 2013

Dear Justin,
sorry for the late answer and acknowledgements... Please see below my

Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabotti at unisa.it
Skype: annam1972
Web page: http://www.unisa.it/docenti/annamarabotti/index

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

>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.

> 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.
I've tried to attach here the files with the images, but the message was filtered out. Please let me know how can I send you the
images. Please take into account that with g_angle command I'm not
analysing multiple dihedrals (or at least, this is not what I'm intended
to do): using the index file .ndx I "told" Gromacs to analyse a
particular dihedral that I defined using a list of the four atoms
composing it. Then, to analyse the three dihedrals of my interest, I
launched three times the command g_angle, and every time I selected a
different dihedral to analyse.
In any case, I repeated the command using the -all flag as suggested,
but nothing changed.
Another strange thing is that the dihedral variation is still between
two fixed values (-200 and 200) instead of 0-360 as I expected to be. Is
this another possible bug or not?
>> >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.
Indeed, when I used xmgrace -nxy, the correct angle value appeared in
the graph. Thanks a lot.
> -Justin
> -- ================================================== 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

More information about the gromacs.org_gmx-users mailing list