VMD-L Mailing List

From: Gupta, S.S. (Somil) (S.S.Gupta_at_uu.nl)
Date: Tue Aug 18 2015 - 04:34:10 CDT

Dear all,
I am new to VMD, and I would like to count the number of H-bonds for each H2O molecule in a configuration of liquid water (xyz format).
can anyone please help with the following:
- what does one use for $sel1, while using a xyz file? Using atom-name like O/H does not help. Or, is there a specific input format the plugin requires?

Also, I have read through the vmd archives that when the donor and acceptor in a hydrogen-bond are same (as in this case both are O-atoms from different molecules)
the results of the plugin may not be reliable. Could anyone please comment if I can try it for my case of liquid water?

Thanks.
Somil