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

[Anna Marabotti]

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

______________________________________________
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabotti at unisa.it
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"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
>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
>DIHEDRAL -OD PROT_DIHDIST.XVG -OV PROT_DIHAVER.XVG -OT
>PROT_DIHTRANS4.XVG -OH PROT_TRHISTO.XVG -OC PROT_DIHCORR.XVG
>
>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