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

From: James Kress <>
Date: Fri, 18 Jan 2019 16:50:55 -0500

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 for more info.

Jim Kress

-----Original Message-----
From: Hai Nguyen <>
Sent: Friday, January 18, 2019 3:46 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] How to load and visualize large trajectories?

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.
AMBER mailing list

AMBER mailing list
Received on Fri Jan 18 2019 - 14:00:04 PST
Custom Search