[gmx-users] g_hbond

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Sep 28 14:53:50 CEST 2012


I have an alcohol system and I want to calculate the number of H bonds
during the trajectory.
My atom type labels are C2-C2-C2-CO-OH-HO.  CO denotes carbon bonded to
oxygen, OH denotes alcohol oxygen, and HO denotes alcohol hydrogen.
In g_hbond how do I specify my groups to consider for H bonding. If I
uses group 0 which is the whole system it says that I have twice as many
acceptors as donors, which shouldn't be the case.



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