how can I extract XYZ from each MD step?

[mbjavan]

Dear ATK users,

is it possible to extract some date such as XYZ of the atomic structure from
each arbitrary step of MD calulation in ATK13.8?
it seems that the option of "export to clipboard" has been considered for this aim. But how does it work?
when i try to add MD configuration from clipboard in builder, there is nothing for showing?

Regards

[Nordland]

The following script would give you the entire MD as a XYZ script:

md = nlread("your_file.nc", MDTrajectory)
md.writeToXYZ("export.xyz")

[mbjavan]

Dear Prof. Nordland,

The following error is seen:

<module>
    md.writeToXYZ("export.xyz")
AttributeError: 'list' object has no attribute 'writeToXYZ'

[Anders Blom]

It should have been

Code: python

md = nlread("your_file.nc", MDTrajectory)[0]
md.writeToXYZ("export.xyz")

Note that the produced XYZ file is not 100% standard - for instance it writes Carbon instead of C and also contains the velocities. Nothing a bit of search and replace can't fix though

[Nordland]

This is not a RASMOL XYZ file. It is the XYZ fileformat for VMD (http://www.ks.uiuc.edu/Research/vmd/) - so you can use it directly to view MD simulations using this program.

[Anders Blom]

At least VMD is tolerant to the extra columns. I'm not 100% sure it accepts "Carbon" instead of "C", however.