[gmx-users] hydrogen bond between polymer and water

[Justin Lemkul]

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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================