Hi,
please help me to read output of gromacs gmx hbond. There are 3 columns: time, h-bonds, and all pairs with no filter on the angle.
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
0 0 0
1000 0 0
2000 2 1
3000 1 1
4000 0 2
5000 3 1
6000 2 0
7000 3 0
8000 4 2
9000 6 3
10000 7 3
11000 7 4
How can the second value (all pairs) be lower than the first one (only H-bonds with the same distance threshold)? Or maybe I misunderstand meaning of the columns - if so, how to imagine the row 4000 0 2, i.e. 1st < 2nd?
Hi Pavel
My understanding is that the program first finds all pair within the 0.35 nm cutoff and then depending on the angle either puts them in column A or B.
So for example at 10,000 ps you have a total of 10 pairs within 0.35 nm of each other, 7 of which also passes the angle cutoff while the remaining 3 do not.
Hi Pavel! You legend in xvg-file is answering your question. The first column is normally the time. The second column is so-called @ s0 is the number of hydrogen bonds. Then you have the third column @ s1 and it shows you pairs. Pairs are the ones found to fulfill certain conditions which you put in your algorithm for calculations or the ones which were there by default (angles, distances etc.). Simply answering your question is that the number you need is in the second column labeled as s0.
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