Sorry if this is a naive question, but I feel a little bit confused about ?NHBOND and ?AVNOHB.
I want to calculate the total number of hydrogen bond between lipid and water and average number of hydrogen bonds per lipid.
Could I just simply say
coor hbond sele resn lip end -
sele resn tip3 end firstu 18 nunit 1 skip 5000
to get the total number of hydrogen bond?
However, I am not sure if I can apply just ?avnohb to get the correct value for number of hydrogen bond per residue. In addition, is it possible with the charmm command to get the standard deviation for that?