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

Erik Marklund erik.marklund at chem.ox.ac.uk
Fri Dec 5 12:05:39 CET 2014

Dear Somadwip,

I see. Assuming that the DNA comes before the ions and water their atoms will have the same indices, in which case you can use the same index file for both analyses. Just make strand_A and strand_B and have g_hbond use those groups, then compare the numbers.

Kind regards,
On 5 Dec 2014, at 10:35, soumadwip ghosh <soumadwipghosh at gmail.com> wrote:

> Dear Erik,
>             I am sorry I dint ask the question properly. Actually I have
> simulated a double stranded DNA with different ions which are expected to
> occupy different grooves of the DNA and break the H-bonds between the DNA
> base pairs of the alternate chains. I want to use the g_hbond utility for
> calculation of h bond length distribution and lifetime. I want to show the
> above h-bonding parameters between chain A and chain B both in presence and
> absence of Na ion. Since g_hbond takes two groups for calculation I am
> unable to understand how to index my groups. Could the use of -b and -e
> flag is useful? How to show that Na is indeed breaking the H-bonds here by
> using g_hbond with proper indexing. If it cannot be shown by g_hbond, is
> there any other way to show it?
> thanks for your time in advance.
> Regards,
> soumadwip Ghosh
> Research fellow,
> Indian Institute of Technology, Bombay
> India
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