[gmx-users] hydrogen bond auto correlation

Michael Brunsteiner mbx0009 at yahoo.com
Tue Jul 1 15:44:18 CEST 2014

Dear all,

I am interested in H-bond life-times and tried to use g_hbond 
with the - ac option
 (gmx 4.6.5) - but i am not sure how to interpret
the outout ... 

1) in the output written to stdout there is a table:

Type        Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2


the entry in column "Rate"  and line "Forward" ... is this the parameter k in equation 10
in the paper from Alenka Luzar (J Chem Phys 113 (23), p10663)??

2) I keep getting a warning "Correlation function is probably not long enough..."
which is not surprising as my system is basically a glass with very slow dynamics ...

... is there a way to estimate the trajectory length I need for this warning to go away

(other than by trial/error)??

thanks in advance for any help!


Why be happy when you could be normal?

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