Re: [AMBER] PCA/ essential dynamics

From: George Tzotzos <>
Date: Tue, 07 Jan 2014 17:14:33 +0100

Recently, January 4, the archived as ANN: MDTraj 0.5.0 Release.

MDTraj 0.5.0 is a python library for manipulating molecular dynamics trajectories. The links for MDTraj 0.5.0 are: (Sources and binary installers) (Documentation and examples)

There is an example of PCA visualisation:



I'm pleased on announce the release of MDTraj 0.5.0, a python library
for manipulating
molecular dynamics trajectories with wide cross-format support and a
focus on speed.

Sources and binary installers can be found at, or
installed via easy_install / pip. Documentation, including many new
examples, can
be found at

A big thanks goes out to Kyle Beauchamp and Ravi Ramanathan for
patches and code reviews.


What's New
- Numerous bug fixes
- Much improved coverage of the test suite.
- Removed cffi dependency for accelerated geometry code
- Faster multi-trajectory loading
- MSMBuilder2 LH5 format support
- Change license from GPL to LGPL
- More convenience methods on Topology
- PDB writer writes connect records
- Hydrogen bond identification with baker_hubbard
- Rotation/translation to superpose trajectories
- New RMSD API. It's much simpler and much more memory efficient
- Full support for computing all of the chi angles
- Add seek/tell methods to all of the trajectory file objects
- New top level memory efficient iterload method for chunked trajectory
On 07 Jan 2014, at 15:53, Andre C. Stiel <> wrote:

> Hi,
> there are a number of questions on essential dynamics analysis and its
> visualization in the mailing list, but I do not get really consistent
> information from it. Most of it seems to be a little outdated. I guess
> there are people using this technique maybe they can guide me to some
> ideas.
> Here is what I gathered from the archive:
> Interactive-ED (IED) ( - from 2004
> running on VMD. I didnt find newer versions or information. And it does
> have some issues with the ptraj format as far as I understand.
> Pocubine plots: VMD plugin, pymol (using modevectors), BILD
> Are there other tools techniques? How do you visualize these movements,
> how compatible are the afore mentioned with the cpptraj formats for
> modes and projections?
> Maybe a little broad question but there is really not to much out there
> on PCA - amber - visualization
> cheers
> And
> _______________________________________________
> AMBER mailing list

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Received on Tue Jan 07 2014 - 08:30:03 PST
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