[gmx-users] calculation of H-bonds

soumadwip ghosh soumadwipghosh at gmail.com
Tue Dec 23 17:24:40 CET 2014


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


More information about the gromacs.org_gmx-users mailing list