Re: [AMBER] How to load and visualize large trajectories?

From: Hai Nguyen <>
Date: Fri, 18 Jan 2019 15:46:26 -0500

On Wed, Jan 9, 2019 at 7:36 AM Chetna Tyagi <> 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)).

For your example:

import pytraj as pt
import nglview as nv
traj = pt.iterload('', '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.
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Received on Fri Jan 18 2019 - 13:00:03 PST
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