# [gmx-users] use of g_hbond

Alexander Law alexander.law at pg.canterbury.ac.nz
Thu Dec 4 08:02:24 CET 2014

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________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of soumadwip ghosh [soumadwipghosh at gmail.com]
Sent: Thursday, December 04, 2014 7:25 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] use of g_hbond

Hello everyone,
I want to calculate the effect of incorporating
ions in the grooves and backbones of a double stranded DNA molecule in the
hydrogen bonding between the two chains constituting the DNA. I want to
calculate the number, distance distribution and the lifetime of H- bonding
between base pairs of two chains both in presence and in absence of the
sodium ion. As far as I know, from the g_hbond utility of GROMACS we can
calculate the hydrogen bond related parameters but I am not quite sure with
the indexing. My index group looks like-

Group     0 (         System) has 97135 elements
Group     1 (            DNA) has   758 elements
Group     2 (             NA) has   624 elements
Group     3 (             CL) has   602 elements
Group     4 (          Water) has 95151 elements
Group     5 (            SOL) has 95151 elements
Group     6 (      non-Water) has  1984 elements
Group     7 (            Ion) has  1226 elements
Group     8 (             NA) has   624 elements
Group     9 (             CL) has   602 elements
Group    10 ( Water_and_ions) has 96377 elements
Group    11 (          major) has   376 elements
Group    12 (          minor) has   256 elements
Group    13 (        chain_A) has   379 elements
Group    14 (        chain_B) has   379 elements
Group    15 (     chain_A_Na) has     1 elements
Group    16 (chain_A_chain_A_Na) has   380 elements
Group    17 (       backbone) has   258 elements

I decomposed the entire DNA molecule into two segments, chain_A and chain_B
so that I can calculate the H-bonding parameters between the two chains.
But I dont know what to do when I want to check the H-bonding between
chain_A and chain_B in presence of sodium. Should I make a separate group
of chainA and Na (say chain_A_Na) and then calculate the h-bonding with
chain_B? Am I doing anything wrong? Is it supposed to be done in some other

Regards,
Senior research fellow,
Indian Institute of Technology, Bombay
India.
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