[gmx-users] lifetime of hydrogen bond

spss4 at iacs.res.in spss4 at iacs.res.in
Thu Jan 2 07:41:41 CET 2020


Dear all
I want to calculate the hydrogen bond lifetime of a dynamic hydrogen  
bond which stays for say 10 ns (as I have saved the trajectory with 10  
ps interval).  I am trying to calculate the lifetime of this hydrogen  
bond by gmx hbond command
gmx hbond -f traj_nopbc.trr -s md.tpr -n index.ndx -num  
hbond_G4_N3_131_N3H4.xvg -dist dist_G4_N3_131_N3H4.xvg -ang  
ang_G4_N3_131_N3H4.xvg -life life_G4_N3_131_N3H4.xvg
Its give me a "uninterrupted hydrogen bond lifetime" plot which stays  
for 200 ps. I cannot understand the meaning of this plot. How to  
explain this 200 ps lifetime?
Thanks
sunipa 


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