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amber netcdf trajectory support #109

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Amber supports MD trajectories to be written in binary netcdf format. Using 
such netcdf is less consuming and hence a support for file format would be a 
good addition to MDAnalysis.

Herewith a test amber top, ascii (.TRAJ) and netcdf (.NCDF) are attached.

Thanks,
Bala

Original issue reported on code.google.com by bala.bio...@gmail.com on 24 May 2012 at 8:48

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GoogleCodeExporter commented 9 years ago 
I prmtop file i added before has some problem. I have attached the correct 
amber topology here.

Original comment by bala.bio...@gmail.com on 24 May 2012 at 8:53

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GoogleCodeExporter commented 9 years ago 
This shouldn't be terribly hard to do. I have read amber netcdf files directly 
into python using netcdf4-python, and have a simple module that writes what I 
believe are correctly formatted Amber netcdf files (VMD recognizes them and 
parses them correctly), although it probably doesn't support all of the 
features. I'm attaching the code as an example. It was adapted from some code I 
found on simtk.org written by John Chodera.

Original comment by joshua.a...@gmail.com on 24 May 2012 at 2:52

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GoogleCodeExporter commented 9 years ago 
Thanks Josh.

Looks doable. How is the code licensed?

Original comment by orbeckst on 24 May 2012 at 5:35

GoogleCodeExporter commented 9 years ago 
Hi Oliver - netcdf4-python is licensed under the MIT license. I don't know what 
license John was using (none listed in the repo), but I think I diverged 
sufficiently and just coded based on the Amber standard, so that shouldn't be 
an issue. The standard that I used was:

http://ambermd.org/netcdf/nctraj.html

I'm not sure if that is the most up-to-date, but pragmatically it seemed to 
work.

Original comment by joshua.a...@gmail.com on 24 May 2012 at 5:46

GoogleCodeExporter commented 9 years ago

Original comment by orbeckst on 28 May 2012 at 4:29

GoogleCodeExporter commented 9 years ago 
This issue was closed by revision c44d84485cf7.

Original comment by orbeckst on 30 May 2012 at 12:08