[gmx-users] hydrogen bond between polymer and water
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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