AMBER Archive (2004)

Subject: Re: AMBER: Software to visualize normal modes!

From: John Mongan (jmongan_at_mccammon.ucsd.edu)
Date: Tue Jun 01 2004 - 18:20:38 CDT

This question gives me an opportunity to announce IED to the AMBER list:

Interactive Essential Dynamics (IED) is a plugin for VMD that enables
easy visualization of results of essential dynamics/principal
component/quasiharmonic analysis and normal modes analysis.

Filtering eigenvectors can be rapidly added or removed from within the
viewer, even while the trajectory is being played. The functional
meaning of an eigenvector can be examined from within the viewer by
dragging the atomic positions along the eigenvector using a slider
control. IED can also draw arrows through atoms to illustrate their
motion along a selected eigenvector when a static visualization is
required (e.g. for publication).

IED reads output from AMBER 8 ptraj, nmode and GROMACS (g_covar and
g_anaeig). It also has (somewhat limited) capabilities to perform PCA on
a trajectory directly (from within VMD).

IED is GPL and freely available from http://mccammon.ucsd.edu/ied

Hope this is useful to people.

To address some of the specific questions:

IED can read nmode output. The vectors file needs to be given a .pev
extension, and you should clear the "Projections file" input box, since
there are no projections. When working with normal modes data, the
trajectory filtering functionality is disabled (since there is no
underlying trajectory to filter), but you can still manipulate the
structure along the modes/vectors.

I haven't tested quasih output. Apparently the ptraj matrix analysis
routines were designed to produce nmode/quasih compatible output
formats, so it may work. If not, you can use the AMBER 8 ptraj (which
will most likely be freely available for non-AMBER 8 users at some
point) or add a quasih format parser to IED. I probably won't be doing
the latter myself as quasih has been retired in AMBER 8.

In principal IED should run on Windows, but I haven't tested it and
getting the environment set up (python, Tkinter, Numpy) may well be more
trouble than it is worth. It was developed on linux and I have reports
of successful use on SGI.

John

On Mon, 2004-05-31 at 21:42, Pradipta Bandyopadhyay wrote:
> Apologies if this is a FAQ.
>
> What is the best freeware to visualize the vectors
> from quasi-harmomic or normal mode analysis using
> quasih or nmode? I have AMBER 7. IED seems to read
> ptraj generated modes - can it be used for quasih
> generated modes?
>
> I would prefer the software which runs in windows
> (SGI or linux will also work).
>
> I would greatly appreciate any suggestion.
>
> Pradipta
>
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