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.
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 Mon Jan 21 2019 - 01:30:03 PST
