I have a netcdf file (prod.nc) that contains time series from a molecular dynamics simulation (Amber force field, OpenMM engine, parmed netCDFReporter). The netCDFReporter had some problems and as a result, the number of frames in the netcdf file is zero. Given below is the ncdump for the file: *$ncdump -h prod.nc <http://prod.nc>netcdf prod {dimensions: frame = UNLIMITED ; // (0 currently) spatial = 3 ; atom = 20504 ;variables: char spatial(spatial) ; float time(frame) ; time:units = "picosecond" ; float coordinates(frame, atom, spatial) ; coordinates:units = "angstrom" ;// global attributes: :Conventions = "AMBER" ; :ConventionVersion = "1.0" ; :application = "AmberTools" ; :program = "ParmEd" ; :programVersion = "3.4.0+11.g1be8ca0f" ; :title = "ParmEd-created trajectory" ;}* However, the netcdf file has non-zero size (that increases linearly with the number of frames stored) which implies that it certainly has the data written into it. I tried a number of tools (nco tools, netCDF4, scipy netcdf reader, xarray) to access the missing data but have not succeeded. *I have two questions:1. Does the file contain real data?2. If the former, is there a way to retrieve the data and create a new netcdf file?* I am desperately looking to salvage near 3 microseconds of simulation data which would take more than 2 months to generate. I would greatly appreciate it if anyone can provide me with some insight into this problem. The attached netcdf file has 14 frames that can be used to examine the issue. Thanks in advance Best Ram
Attachment:
prod.nc
Description: Cdf file
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