From: hamid mosaddeghi (
Date: Mon Mar 07 2011 - 13:20:13 CST

Dear all

I work with bulk water (SPC/E) and need to calculate Hbond, I used VMD
for this purpose,

for calculation Hbond (extention ----> Hydrogen .... ---->find
hydrogrn bond)  I used cutoff angle

30 and cutoff distance 3.5.

then I calculate (number of hbond)/(number of water moleclue)= 1.27 ,
then I multiply it in 2

(beacause hbond share between two water molecule) ,then  it equal ~2.6
but it is small of data

reported in paper for spc/e water (3.2) why? please help me.

if I used cutoff angle 45 instead 30 ,I get it equal=3.2 , is it correct?

what maximum cutoff angle?

thanks in advance