[gmx-users] g_angle - fraction of trans dihedrals
Repakova Jarmila
jar at fyslab.hut.fi
Thu Dec 15 16:33:55 CET 2005
Hello,
as mentioned in reference for g_angle, the calculation of the fraction of
trans dihedrals " is probably only fun for a selected few ". Nevertheless, I
came across such figures couple of times in articles, when gromacs was used
for analysis. So, I decided to ask you about the possible bug in these
calculations (I'm using gromacs version 3.2.1):
I wanted to calculate the fraction of trans dihedrals for lipid acyl chains
as a function of time and also as a function of distance from some other
molecules. Thus, I wrote my own script and in order to check my results I
compared the data over all lipids in my system with the output from g_angle.
My values for trans-fraction were rather higher than the values obtained
from g_angle.
To find out where is the error, I run a short 10ps dynamics of single butan
molecule in water (only one dihedral angle, for simplicity). At the end of
this email I copied the resume of results I got from g_angle and using my
script. As you can see, the values of dihedral angles (2. and 4. column)
computed by the two methods are the same (remark : I use the values of
dihedral angle in the range 0-180, whereas g_angle uses the range 0-360; thus
when ang_g>180 => ang_my=-ang_g, and from the point of view of fraction of
trans conformations ang_g=-ang_g).
But, if you look at 3.column you see, that g_angle use probably the wrong
condition when deciding whether the dihedral is in trans conformation or not
(or before this, there should be the correction of dihedral angle so that it
fall within the range 0-180degrees). When the ang_g > 180, then the
conformation is not considered to be 'trans', which might be bug.
In case anybody is interested in, I'm also attaching the original files
butan-MD.gro, dihfrac.xvg, angaver.xvg obtained from g_angle and the results
from my script are in trans-dihedrals.dat.
Best regards,
Jarmila Repakova
Biological Physics and Soft Matter Group
Laboratory of Physics, Helsinki University of Technology
=====================================================
#time[ps] ang_g frac_g ang_my frac_my
0.0 176.787 1.0 176.787 1.0
0.2 177.888 1.0 177.888 1.0
0.4 172.714 1.0 172.714 1.0
0.6 162.979 1.0 162.979 1.0
0.8 172.709 1.0 172.709 1.0
1.0 166.143 1.0 166.143 1.0
1.2 180.063 0.0 179.936 1.0
1.4 173.118 1.0 173.118 1.0
1.6 168.687 1.0 168.687 1.0
1.8 175.83 1.0 175.829 1.0
2.0 167.27 1.0 167.27 1.0
2.2 166.992 1.0 166.992 1.0
2.4 175.582 1.0 175.582 1.0
2.6 184.409 0.0 175.591 1.0
2.8 188.532 0.0 171.468 1.0
3.0 189.196 0.0 170.804 1.0
3.2 195.746 0.0 164.254 1.0
3.4 182.321 0.0 177.679 1.0
3.6 177.45 1.0 177.45 1.0
3.8 174.832 1.0 174.832 1.0
4.0 188.514 0.0 171.486 1.0
4.2 143.461 1.0 143.461 1.0
4.4 157.821 1.0 157.821 1.0
4.6 161.254 1.0 161.254 1.0
4.8 153.955 1.0 153.955 1.0
5.0 164.918 1.0 164.918 1.0
5.2 168.109 1.0 168.109 1.0
5.4 176.384 1.0 176.384 1.0
5.6 174.139 1.0 174.139 1.0
5.8 179.234 1.0 179.234 1.0
6.0 180.0 1.0 179.991 1.0
6.2 184.341 0.0 175.659 1.0
6.4 189.884 0.0 170.117 1.0
6.6 203.065 0.0 156.935 1.0
6.8 178.625 1.0 178.625 1.0
7.0 190.744 0.0 169.256 1.0
7.2 178.536 1.0 178.536 1.0
7.4 171.087 1.0 171.087 1.0
7.6 178.055 1.0 178.055 1.0
7.8 177.152 1.0 177.152 1.0
8.0 176.632 1.0 176.632 1.0
8.2 163.397 1.0 163.397 1.0
8.4 173.533 1.0 173.533 1.0
8.6 168.501 1.0 168.501 1.0
8.8 172.021 1.0 172.021 1.0
9.0 176.344 1.0 176.344 1.0
9.2 187.81 0.0 172.19 1.0
9.4 196.573 0.0 163.427 1.0
9.6 179.622 1.0 179.622 1.0
9.8 175.814 1.0 175.814 1.0
10.0 183.291 0.0 176.709 1.0
-------------------------------------------------------
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