Re: [AMBER] Partial frame/traj dump during MD run.

From: Dr. Anselm Horn <>
Date: Mon, 29 Nov 2021 12:18:01 +0100


as a first quick response to your question:
Amber can write a restart file with coordinate information to the disk
(see input parameter ntwr , Amber21 manual p. 364); together with the
topology file this can be used either directly for visualization or for
conversion to a pdb file.
Amber also can dump molecular properties (energies, temperature etc) to
an info file and update that as well.

A direct pdb file dump, however, is not supported by Amber, as far as I
know. I guess all this is mostly due to performance (frequent writing to
disk slows down your MD significantly) and precision (atomic coordinates
in pdb format have a limited precision).

You may simply use the already written trajectory files for a
visualization and analysis while the MD is still running.
(Since most application jobs probably run for days than just for
hours/minutes, direct visualization is not that important IMHO.)

But the Amber experts and developers might want to chime in here.

Best regards,


Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

On 11/29/2021 11:52 AM, Pedro Guillem wrote:
> Hello all,
> I was wondering if amber20 is able to periodically dump intermediate
> frames/traj/energies to a PDB file during an MD run. The question has to do
> with getting snapshots of partial results as the process runs.
> I know this is possible with CHARMD and NANMD (under Discovery Studio).
> Partial frames are stored and updated periodically at the UI and the user
> gets to see changes every few seconds.
> Rosetta also ships a Pymol plugin (by Baugh, etc al) that updates a remote
> pymol UI session during MD runs, so you can visually see what's going on as
> computations occur.
> If not yet available, writing a few lines to dump trajectory/energy/frame
> data wouldn't take much effort. I'm sort of new to the amber code, so I
> wouldn't have a clue on where to embed a probe during a running MD (I'm
> guessing the pmemd/sander source?). I would gladly do so.
> Thanks in advance for any hints.
> Pedro
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Received on Mon Nov 29 2021 - 03:30:03 PST
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