[gmx-users] Regarding viewing Trajectories

[Dilip H N]

Thamk you ,
But in my RDF i have got a peaks(solvation shells) with Carbon of amino
acid with ammonia in ammonia-water mixture, so i need to analyse why that
peak has been formed, which can be viewed by visualizing the trajectories
 in vmd.
So i need to see that at what time frame/step has the bond
formed/particular molecule is closer to the preferred atom, since with this
i can give justification to my results...
So how can i view those molecules that have been more closer/bond formation
with specific molecule has occurred...since viewing the whole trajectory
time frame (i have 6002 frames) is time consuming...
I wrote in Graphical representation > selected atoms > all within 5 of
protein and i am viewing it for every time frame...



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On Wed, Apr 5, 2017 at 12:07 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> A peak in a distance distribution function by definition is contributed to
> by lots of molecules around that distance from lots of different central
> points. There's no single frame for each point.
>
> If you look at a normal histogram, and see a peak, asking "which single
> data point made this" is not meaningful, because multiple data points have
> normally contributed.
>
> Mark
>
> On Wed, Apr 5, 2017 at 6:40 AM Dilip H N <cy16f01.dilip at nitk.edu.in>
> wrote:
>
> > Hello.,
> > In RDF of amino acid with ammonia and water mixture, i have got a 1st
> peak,
> > 2nd peak (solvation shell), and i need to view this in the vmd by making
> > use of the trajectories (trr/xtc files), so while viewing the
> trajectories
> >
> > 1] how can i view that exact trajectory at which i have got the
> particular
> > peak in RDF (since that would mean either H-bond formation/probability of
> > tht molecule close to that)
> > because viewing each frame to find it would take literally lot of time,
> ...
> >
> > Thank you.
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
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> > <
> > https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student