[gmx-users] H-bond query

[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?
Furthermore, in the hbnum.xvg file the third column represents the no.
of H-bond within the distance cut-off and the 2nd one is the total no
of hydrogen bonds as a function of simulation time. So, which one
should I plot in this case against time?


Your help is required.


Soumadwip
Research Fellow
IITB
India