[gmx-users] Regarding analysing cos theta distribution functions

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 12 10:05:47 CEST 2017


Hi,

Thanks Joao! I don't know whether all the necessary infrastructure exists
for this particular task, but the general workflow using GROMACS tools
might include stages like

gmx mk_angndx to get index files
gmx angle to compute the angles of interest using those index files
gmx analyze to get distribution functions of those angles

Mark

On Wed, Apr 12, 2017 at 9:54 AM João Henriques <joao.m.a.henriques at gmail.com>
wrote:

> 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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> > > Ph.D Student
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