[gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function

Dilip H N cy16f01.dilip at nitk.edu.in
Wed Jul 26 19:04:44 CEST 2017

Hello all,
i am trying to make the indexing of groups by gmx make_ndx in order to
calculate hydrogen bond autocorrelation function.
I have glycine and water mixture...in the gmx make_ndx manual it tells tht
OH and NH groups are regarded as donors and  O, N being acceptor...but how
can i make those donors indexes..
but i dont have any OH or NH groups in glycine,water mixture...
how can i resolve this, with set of commands for indexing...

Thank you..

With Best Regards,

Ph.D Student

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