[ase-users] ASE-Amber interface

[Ask Hjorth Larsen]

Hi Markus,

Would you be able to help with this?  Is Amber very closely related to
the NetCDF format?

Best regards
Ask
Am Do., 9. Aug. 2018 um 12:21 Uhr schrieb Charles-Alexandre Mattelaer
via ase-users <ase-users at listserv.fysik.dtu.dk>:
>
> Dear ASE community
>
> I was wondering if someone could help me getting the ASE-interface working properly? Following the example of 2 H2O ( https://wiki.fysik.dtu.dk/ase/ase/calculators/amber.html ) I keep getting the following error (which according to a google search has is related to scipy) :
>
> /usr/lib/python2.7/dist-packages/scipy/io/netcdf.py:297: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.)
>   ), category=RuntimeWarning)
>
> I literally copy-pasted the input files from previously mentioned website, so I'm a bit lost since I have no very little python knowledge. Could i write the coordinates in another format than netcdf?
>
> Kind regards and thanks in advance
>
> Charles-Alexandre Mattelaer
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