[gmx-users] Regarding analysing cos theta distribution functions

Wed Apr 12 10:28:49 CEST 2017

Hi,

There's lots of options... see
http://manual.gromacs.org/documentation/2016.3/user-guide/cmdline.html#commands-by-topic
for
starters.

Mark

On Wed, Apr 12, 2017 at 10:06 AM Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> Thank you Mark, João Henriques.
> I have ran a Md simulation of amino acid in water solvent mixture.
> In gromacs what are all the analysis i can do with my system (amino
> acid-water solvent mixture)..??
> For eg., I have just calculated RDF (to knw how atoms are distributed
> radially around each other),
> apart from this what are the analysis part tht i can do with gromacs..??
>
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
>
> On Wed, Apr 12, 2017 at 1:23 PM, 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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> > > > --
> > > > 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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