[gmx-users] hydrogen bond between polymer and water

Justin Lemkul jalemkul at vt.edu
Wed Jul 18 23:14:26 CEST 2012

On 7/18/12 4:57 PM, zifeng li wrote:
> Dear Gromacs users,
> I am calculating hydrogen bonds between polymer and water using
> Gromacs 4.5.4 and opls-AA force field. Our goal is to extract
> coordinates of atoms which form hydrogen bond at each frame.
> 1. The way I do it now is iterating following commands at every frame
> using a script:
> g_hbond -f  fn -s fn  -b frame#  -e frame# -g frame#
> trjconv -f  fn  -s fn -b frame#  -e frame#  -o frame#.pdb
> It works but  would take 5ns and generate 0.6GB data per 100 frame for
> my system.
> Since Gromacs can calculate the hbond life time so that I wonder is
> there anywhere I can find  hbond index for each frame?

One run through g_hbond with -hbm and -hbn will map out all hydrogen bonds and 
when they exist.  No need to analyze frames separately.

> 2. Another thing weird in my simulation is : based on the hbond log
> file, all the hydrogen that can form hbond is HW1, which is the first
> hydrogen in water residue. a glimpse of my log file:
> #      Donor      Hydrogen      Acceptor
>    SOL750OW      SOL750HW1     BAE380O1
>    SOL787OW      SOL787HW1     MMA491O1
>    SOL824OW      SOL824HW1     MMA423O1
>   Would you have any idea about this?

The default behavior of g_hbond is to merge equivalent hydrogens (-merge flag) 
so HW1 and HW2 are considered the same and likely are just labeled as HW1.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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