[gmx-users] gmx hbond

[Smith, Micholas D.]

You could use gmx select to create an index file containing water molecules obeying these criteria at each time-step, and then use gmx hbond for for each index (being sure to only look at the relevant frame only).


Something like this:


gmx select (your commands here to generate an index index file for each frame).


Then use a loop like so:

#where I assume index 0 is the amino acid you are interested in


for((i=1;i<$MAXFRAMES_SELECTION;i++)); do

echo "0 \r $i" | gmx hbonds -num -r 0.2 -b "$i" -e "$i"  -n index_file_containing_waters_at_2Ang_at_each_frame.ndx; sed -e '/\#/d' - '/\@/d' -e '/\&/d' hbnum.xvg >>hbnum_2Ang.dat; rm hbnum.xvg ;done


Make a new index file for the 0.2 to 0.4 Ang and repeat.


-Micholas


===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of paul buscemi <pbuscemi at q.com>
Sent: Sunday, January 6, 2019 12:41:41 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gmx hbond

Use VMD/extensions/hydrogen bonds

> On Jan 6, 2019, at 11:01 AM, rose rahmani <rose.rhmn93 at gmail.com> wrote:
>
> hi,
>
> I want to know the number of hydrogen bonds of amino acid with water in
> different distances above surface. for example in first 0.2nm, in second
> 0.2 nm(0.2-0.4 nm) above surface. how can i do it by gmx hbond? I couldn't
> find any proper option for that.
>
> best
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