[gmx-users] Hydrogen Bond in Water SPC by g_hbond

Ester Chiessi ester.chiessi at uniroma2.it
Fri May 21 14:56:27 CEST 2004


During the analysis of hydrogen bond in water SPC, I ran g_hbond using
-shell 0.7 and the default definition of the hydrogen bond, for an NVT
ensamble of water SPC equilibrated at 303 K.
I calculated the number of hydrogen bond 'per' water molecule by dividing
the number of HB's for the number of acceptors (obtained by the option -da
). The resulting value is about 1.4 HB/water molecule, quite lower than
those expected.

1) Can I consider this procedure as correct for the evaluation of the
number of hydrogen bond 'per' molecule, in the case of water? The results
could be correct applying a factor of 2.

I think the discrepancy is too high for ascribing it to an edge effect
related to the option -shell.

If I remove the angular cutoff (using -a 180), I obtain about 3 HB/water

2) Is the default definition of HB unsuitable for water or is there
someting wrong in my system ( a rectangular box of 1142 molecules sized
2.5X3.8X3.8 nm^3 ) ?
Gromacs V. 3.1.4.

Any comment is appreciated.


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