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

Justin Lemkul jalemkul at vt.edu
Fri Sep 27 16:23:40 CEST 2013

On 9/27/13 8:18 AM, Anna Marabotti wrote:
> 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
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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
>> 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

You need to upload images to public sharing sites and provide a URL.

> 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.

OK, that sounds a lot different from the initial report :)  Makes sense.

> In any case, I repeated the command using the -all flag as suggested,
> but nothing changed.

Can you please show us what this means?  A snippet of output here would be useful.

> 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?

No, that's not a bug.  Dihedrals can range equivalently from -180 to 180 or 0 to 
360.  Given that (I believe) the code deals in terms of the cosine of angles, 
the -180 to 180 range is intuitive.  You can easily perform a simple 
transformation if you prefer that the values fall within the 0 to 360 range.



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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