[gmx-users] Degree of hydrogen bonding

Udaya Dahal dahal.udaya at gmail.com
Wed May 7 00:05:56 CEST 2014

Hi all,

I am simulating a PPO chain in water. I am looking for the degree of
hydration. Currently, I am using n=27 monomer CH3-(O-CH(CH3)-CH2)n -O-CH3.
I have total 4046 water molecules in a box of 5 5 5.
When I use the g_hbond it says it gives the hydrogen bond and the pairs in
(0.35nm) distance. As it seems it gives the total hydrogen bonds in the
system. I am wondering if there is a way to calculate the total numbers of
h-bond between the polymer and the water.

Since I am not familiar with the programming language( reading the huge
code is out of question for the time being). The model is the atomistic one
and and the water i am using is spce.  Also how do the boundary bonds are
calculated since for a small box, the omission of the boundary bonds will
completely alter the property.

Udaya Dahal

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