[gmx-users] Re : using g_hbond between index gps of specific interest

[soumadwip ghosh]

Dear Erik,
             I am sorry I dint ask the question properly. Actually I have
simulated a double stranded DNA with different ions which are expected to
occupy different grooves of the DNA and break the H-bonds between the DNA
base pairs of the alternate chains. I want to use the g_hbond utility for
calculation of h bond length distribution and lifetime. I want to show the
above h-bonding parameters between chain A and chain B both in presence and
absence of Na ion. Since g_hbond takes two groups for calculation I am
unable to understand how to index my groups. Could the use of -b and -e
flag is useful? How to show that Na is indeed breaking the H-bonds here by
using g_hbond with proper indexing. If it cannot be shown by g_hbond, is
there any other way to show it?

thanks for your time in advance.

Regards,
soumadwip Ghosh
Research fellow,
Indian Institute of Technology, Bombay
India