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

Erik Marklund erik.marklund at chem.ox.ac.uk
Fri Dec 5 10:30:08 CET 2014

Dear Soumadwip,

If you want to interrogate the interactions with Na you need to use the -contact flag with g_hbond if I recall correctly since Na is not recognised as a bond donor/acceptor. I'm not entirely sure what you want to achieve however, so I'm not sure I answered your question.

Kind regards,

Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

On 5 Dec 2014, at 04:22, soumadwip ghosh <soumadwipghosh at gmail.com<mailto:soumadwipghosh at gmail.com>> wrote:

Hello everyone,
                       I am re sending my mail since I did not understand
the suggestion provided last time. I want to calculate the effect of
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
ways? Please help me out with this.Thanks in advance.

Soumadwip Ghosh
Senior research fellow,
Indian Institute of Technology, Bombay
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