[gmx-users] Regarding analysing cos theta distribution functions

[Dilip H N]

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....



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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