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 11303/11303
Normalization for c(t) = 0.0615891 for gh(t) = 1.23179e-06
Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#
Hydrogen bond thermodynamics at T = 300 K
Fitting parameters chi^2 = 3.03095
Q = 0
------------------------------ --------------------
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 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.
Which value should I take, since application of pbc gives a different value than that of the original trajectory value of lifetime.?
Mrs/Miss Chand,
The answer to your question depends on which properties you would like to study - the bonding ability of isolated molecule or of the ensemble of molecules in the crystal?
You may consider the value which obtained after pbc correction. Though, it appears something weird.! Which version of gromacs your using? by seeing your command (g_trjconv) I assume it is 4.6 and below. There might be some bug which might be updated in the newer version.
Ofcourse always consider the value after applying PBC, If your system is periodic and PBC was applied during simulation.
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