[gmx-users] hbond correlation function

Erik Marklund erikm at xray.bmc.uu.se
Fri Oct 22 11:03:38 CEST 2010

Navjeet Ahalawat skrev 2010-10-22 10.46:
> Hi.. all
> I would like to calculate the hydrogen bond correlation function
> C(tau) for protein water hbonds and water-water hbonds. In the manual
> it is written that using g_hbonds one can calculate C(tau), however it
> does not say clearly how to calculate the C(tau) between different
> groups present in the system for e.g. protein-water, water-water etc.
> Any help in this regard would be highly appreciated.
> Thanks and regards,
> Navjeet Ahalawat
It finds the hydrogen bonds between the groups that you select, then 
uses the resulting hydrogen bond existence function to calculate C(tau). 
In other words, just select the index groups you want and g_hbond will 
compute the corresponding acf.


Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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