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

soumadwip ghosh soumadwipghosh at gmail.com
Fri Dec 5 13:31:07 CET 2014

Dear Erik,
             Thats how I have calculated the h-bond number and
distributions between chain_A and chain_B .Is there a way to freeze Na in
chain A(say) and then calculate the h-bonding with chain_B? I hope you get
that I want to calculate the h-bonding between chain_A and chain_B in
presence of sodium as well. Now how to do that? Will it be useful if I
calculate h -bonding at different time gaps using -b and -e flags assuming
that the system will be more perturbed by sodium towards the end the
simulation?Is it required to incorporate Na ions in any of the chain by
group merging? Or there is an alternate way out?

Thanks for your time.


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