[gmx-users] hydrogen bond between polymer and water

zifeng li lizifeng7 at gmail.com
Wed Jul 18 22:57:12 CEST 2012

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?

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?

Thanks in advance!


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