[gmx-users] calculation of H-bonds

[soumadwip ghosh]

Dear all,
            my project involves around the interaction of DNA with small
molecules. I want to calculate (rather show) the native H-bond breaking of
a double stranded DNA in the presence of three ions. Some of my ions are
capable of making secondary H bonds and I want to show that as well. My
question is how g_hbond can be used specifically to make a comparison of
above kind.I have taken atoms of two chains of the DNA constituting the
grooves and indexed them. How to interpret native H-bond breaking or
additional H-bond forming? Is the -shell option useful? Also how can one
estimate the lifetime of these H-bonds using the -ac option? Any kind of
help in this regard will be hugely appreciated.

Thanks in advance for your time.

Soumadwip Ghosh
Research scholar
Indian Institute of Technology, Bombay
India