[gmx-users] Regarding analysing cos theta distribution functions

[João Henriques]

He wants to compute the angular distribution functions, ADFs (water-water
O-H vector), of the first hydration layer. I have posted a similar question
(twice, under different formulations) some time ago and got no help. I'd
suggest experimenting with MDAnalysis (python module), because default
gromacs tools are unlikely to do the job without some creative
hacking/quick-and-dirty scripting.

Re-ordering the water molecules by proximity to the protein surface (per
snapshot) is easy (use gmx trjorder) and establishing the hydration layer
cutoff is also relatively simple (use gmx rdf). Getting the ADFs in the
proper way is not easy/practical. At least I didn't find it easy at all
(and I'm not alone in this). MDAnalysis makes things easy and customizable,
but it can be rather slow.

See the link below for some examples. I ended up using bits and pieces of
the class MDAnalysis.analysis.waterdynamics.AngularDistribution until I got
the desired result.

https://pythonhosted.org/MDAnalysis/documentation_pages/analysis/waterdynamics.html

Good luck!

/J


On Wed, Apr 12, 2017 at 8:19 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> I have no idea what a cos theta distribution is, nor the objective of your
> study, so it's hard to help. But gmx mk_angndx is intended to help with
> such cases.
>
> Mark
>
> On Wed, Apr 12, 2017 at 8:17 AM Dilip H N <cy16f01.dilip at nitk.edu.in>
> wrote:
>
> > Hello Jonathan,
> >
> > Suppose i want to calculate the cos theta distribution of hydrogen's of
> > water  in 1st hydration shell of amino acid (glycine)
> > ie., orientation of  alpha carbon of glycine with oxygen of water
> > molecules... how can i calculate it..??
> >
> > And in  what groups/atoms should i make the indexes..?? (like it says the
> > index file must contain atom triplets for angles)...
> > How to make the atom triplets.. which atom the cos theta is to be found
> out
> > should be placed in the indexing order.. so to find the
> > angle between alpha carbon of glycine with oxygen of water molecules....
> >
> >
> >
> >   <https://mailtrack.io/> Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> >
> > On Wed, Apr 12, 2017 at 11:12 AM, Jonathan Saboury <jsabou1 at gmail.com>
> > wrote:
> >
> > > For making .ndx files look at the following:
> > > http://manual.gromacs.org/programs/gmx-make_ndx.html
> > >
> > > Best of luck,
> > > Jonathan
> > >
> > > On Tue, Apr 11, 2017 at 10:26 PM, Dilip H N <cy16f01.dilip at nitk.edu.in
> >
> > > wrote:
> > >
> > > > gmx sorient -f .xtc/trr -s .tpr -n .ndx...
> > > >
> > > > How to make these indexes for this case..?? what are the atoms/groups
> > > > that i need to consider for
> > > >
> > > > indexing in this case..
> > > >
> > > >
> > > >
> > > >
> > > >   <https://mailtrack.io/> Sent with Mailtrack
> > > > <https://mailtrack.io/install?source=signature&lang=en&
> > > > referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
> > > >
> > > > On Wed, Apr 12, 2017 at 9:57 AM, Dilip H N <
> cy16f01.dilip at nitk.edu.in>
> > > > wrote:
> > > >
> > > > > Hello,
> > > > > 1] I want to calculate  cos theta distributions (eg.,cos theta
> > > > > distributions of hydrogen's of water in first hydration shell layer
> > of
> > > > > amino acid)..??
> > > > > 2] and how can i analyze the graph ..??
> > > > > --
> > > > > With Best Regards,
> > > > >
> > > > > DILIP.H.N
> > > > > Ph.D Student
> > > > >
> > > > >
> > > > >
> > > > >   <https://mailtrack.io/> Sent with Mailtrack
> > > > > <https://mailtrack.io/install?source=signature&lang=en&
> > > > referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > With Best Regards,
> > > >
> > > > DILIP.H.N
> > > > Ph.D Student
> > > > --
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> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
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