[gmx-users] how to use the triplets index file generated by g_hbond

Yun Shi yunshi09 at gmail.com
Sat May 5 19:22:54 CEST 2012

Hello all,

I have used g_hbond with -hbn option to generate a .ndx file that has
Acceptor - Donor - Hydrogen in each line of the last index group.

But I wonder I could I use this index file to monitor each hydrogen bond
specified by these triplets along the trajectory?

Also, I understand that the -ins in no longer available. But how can we
analyze those water-mediated hydrogen bonds?

Thanks for any suggestion,

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