[gmx-users] use of g_hbond

Alexander Law alexander.law at pg.canterbury.ac.nz
Thu Dec 4 08:01:56 CET 2014


You may benefit from the make_ndx command. This allows to make a custom index group and you can add individual atoms as 1 group with only one element.


Also, I recommend you decide on a time cut off points using -b (start) -e (end) these will be in frame 

To decide on which ion you want to use pick a single frame which interests you and use this command:

grompp -s .pdb -f .xtc -dump (interest frame).pdb

>From there you can see which ion atoms you pymol or coot and then make you custom index group

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
ways? Please help me out with this.Thanks in advance.

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