[gmx-users] Regarding viewing Trajectories

[Mark Abraham]

Hi,

On Wed, Apr 5, 2017 at 3:26 PM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Thamk you ,
> But in my RDF i have got a peaks(solvation shells) with Carbon of amino
> acid with ammonia in ammonia-water mixture,


I don't understand how an ammonia-water mixture has amino-acid carbons in
it. Please describe your system and RDF accurately the first time.

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...
>

"Justify" doesn't seem like the right word. You can add a physical
interpretation to what you've computed, once you're sure you've computed
the thing you want. But doing so only makes sense if it relates to the aim
of your study, which is kind of your business to already know before you
start computing things. :-)

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...
>

Then either every frame contributes (e.g. you have lots of carbon atoms and
lots of ammonia and a lot of the RDF is in that first peak, so there is a
very low chance that any frame has zero carbon atoms close to any ammonia
atom), or you haven't been specific enough in describing to VMD what you
actually want.

Mark


>
>
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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
> > >
> > >
> > >
> > >   <https://mailtrack.io/> Sent with Mailtrack
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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
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