[gmx-users] Regarding analysing cos theta distribution functions

[Mark Abraham]

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@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
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> > > 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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