On Mon, Jan 21, 2019 at 4:22 AM Chetna Tyagi <cheta231.gmail.com> wrote:
> Dear all,
>
> Thanks for all the suggestions.
>
> This is in reply to Prof. Nguyen. I had tried NGLview before. It results in
> upload of the trajectory alright but the viewer is left blank. I tried few
> times to solve this problem but I couldn't.
>
>
Hi Chetna, is it possible to share a chunk of data (offline) with your
commands so I can try to debug?
Please do feel free to post your question in nglview page:
https://github.com/arose/nglview/issues
Hai
> And in response to Prof. Kress, I use VMD only on a Linux machine and yet I
> encountered such a problem. The first suggestion of uploading only a subset
> (using Stride count) of trajectory worked for me as I could
> see the movement of peptide with respect to the membrane.
>
> Secondly, Prof. Roe's suggestion to remove just the hydrogens from water
> helped to reduce it's size from 85 GB to 17 GB which is great.
>
> Thank you again. Regards
> -Chetna
>
> On Fri, Jan 18, 2019 at 10:51 PM James Kress <jimkress_58.kressworks.org>
> wrote:
>
> > VMD needs a large amount of memory for large (many frame) trajectory
> > display. 16 GB is far too little. Also, the Windows version is limited
> by
> > the fact VMD is a 32 bit application.
> >
> > Try VMD on a Linux machine with more RAM.
> >
> > Post your question here vmd-l.ks.uiuc.edu for more info.
> >
> > Jim Kress
> >
> >
> > -----Original Message-----
> > From: Hai Nguyen <nhai.qn.gmail.com>
> > Sent: Friday, January 18, 2019 3:46 PM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] How to load and visualize large trajectories?
> >
> > On Wed, Jan 9, 2019 at 7:36 AM Chetna Tyagi <cheta231.gmail.com> wrote:
> >
> > > Dear all,
> > >
> > > This is not specifically an AMBER question but I would like to ask how
> > > can we visualize large trajectories?
> > >
> > > I carried out three separate accelerated MD runs of 500 ns each. I
> > > want to see how my peptide eventually interacts with the lipid bilayer.
> > > When I load it in VMD for visualization, the program just stops with
> > > an error like "Can't load any more frames".
> > >
> > > Is it a problem with VMD or that my computer's memory (16 GB) is
> > > insufficient? I could not find similar errors on VMD help forums.
> > >
> > >
> >
> > > What are some other software or tools to visualize this? How did you
> > > solve this problem?
> > >
> >
> > You can check nglview (use pytraj (Python API of cpptraj)) to visualize
> > very
> > very large (few hundreds GB or TB) trajectory)).
> > https://github.com/arose/nglview
> >
> > For your example:
> >
> > import pytraj as pt
> > import nglview as nv
> > traj = pt.iterload('your.nc', 'your.prmtop') # Must use iterload to
> create
> > on-disk trajectory view = nv.show_pytraj(traj) view #
> >
> > Downside: nglview is not (yet) as powerful as VMD, and you need to use it
> > in
> > Jupyter notebook.
> > Hai
> > _______________________________________________
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> >
> >
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> >
>
>
> --
> Best wishes
> Chetna
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Received on Tue Jan 22 2019 - 21:00:02 PST
