[gmx-users] H-bonding

[soumadwip ghosh]

Hello all,
             I am trying to see what happens to the no. of Watson-Crick
hydrogen bonds between two parallel chains of a double stranded DNA on
incorporating a flat graphene sheet. The no of interchain H-bonds are
supposed to decrease with time. But I am not sure how to use g_hbond in
order to demonstrate this. How should I make index groups for the two
chains of DNA? Should I take all the atoms into account (except backbone)
and then index them like chain_A and chain_B and then analyze the hbnum.xvg
file from g_hbond?

Your help is required.

Soumadwip
Research Fellow
IITB
India