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
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.
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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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