[gmx-users] Regarding analysing cos theta distribution functions
Dilip H N
cy16f01.dilip at nitk.edu.in
Wed Apr 12 11:57:40 CEST 2017
Thank you,
for calculating the angle distribution, I gave the following command (for
glycine-water mixture molecule) as
gmx mk_angndx -s md.tpr -n angle.ndx
and i got the following indec file as..
[ UB_th=109.5_368.192f ]
2 1 3 2 1 4 3 1 4
[ UB_th=109.5_251.042f ]
2 1 5 3 1 5 4 1 5
[ UB_th=107.5_430.952f ]
1 5 6 1 5 7
[ UB_th=110.0_365.682f ]
1 5 8
[ UB_th=115.0_301.252f ]
6 5 7
[ UB_th=109.5_418.402f ]
6 5 8 7 5 8
[ UB_th=118.0_334.722f ]
5 8 9 5 8 10
[ UB_th=124.0_836.802f ]
9 8 10
What does the UB_th.... mean here..??
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On Wed, Apr 12, 2017 at 1:58 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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 at 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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> > DILIP.H.N
> > Ph.D Student
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--
With Best Regards,
DILIP.H.N
Ph.D Student
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