[gmx-users] Fwd: Difference in Hydrogen Bond Lifetimes on using pbc

Apramita Chand apramita.chand at gmail.com
Wed Aug 30 08:07:08 CEST 2017

Dear All,
I've carried out a 100ns simulation of protein in water and want to
calculate hydrogen bond (forward) lifetime between Protein-Water.

 I tried g_trjconv with application of -pbc mol -ur compact options on
untruncated(100ns) trajectory. The results came as:

*ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) =
1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 =    3.03095Q
=          0--------------------------------------------------Type
Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2Forward         0.001
1793.775      23.259     3.03095*
When I tried the same with the original unconverted trajectory(without
g_trjconv ,without pbc options), I got a lifetime of *2345.890ps*.

*My question is ,*

*Which value should I take, since application of pbc gives a different
value than that of the original trajectory value of lifetime.*
I would be very grateful for your help.
Looking forward to your suggestions

Yours sincerely
Apramita Chand

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