On 11/10/13 7:18 PM, bharat gupta wrote:
I checked the file hbnum.xvg file and it contains three columns - time,
hbonds, hbonds that donot follow the angle criteria. In that case SS1 is
The third column is not actually H-bonds, then ;)
the average of actual hbonds (2nd column ) and SS2 is the average of 3rd
column. Am I right here or not ??
Yes.
I tried to calculate the h-bond for residues 115-118 individually, and then
checked the average for each residue. For single residue calculation, the
g_analyze average value is correct.
But when I calculate the h-bond as a range 115-118, I get the g_analyze
value as 1.62 . I calculated the average manually in excel, got the average
values as 16.2 [which is (g_analyze avg value)/10].
That is impossible. You cannot get a different average by examining the same
numbers. Read the g_analyze output again - I am willing to bet that you're not
seeing the exponent of the scientific notation.
I then added up the average values of h-bonds of individual residues and
the final comes around 16.2, same as that of the 115-118 range h-bonds.
This means that my calculation is correct.
I also used trjorder to calculate h-bond at distance 0.34 for residues
115-118. I got the average value around 2.51 from g_analyze, where as
manual calculation gives 25.1. I don't knw why for the range the g_analyze
give avg as (actual avg value)/10 ??
Why does trjorder and g_hbond gives different number of hydrogen bonds for
the same residue set??
All of this comes down to correctly reading the screen output. I have no idea
what you're doing with trjorder, though. It doesn't measure H-bonds.
-Justin
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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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