VMD-L Mailing List

From: Giuseppe La Rosa (giuseppe.la.rosa_at_tum.de)
Date: Fri Nov 07 2014 - 07:51:26 CST

Amber14 (and probably also some version before) is able now to output also
restart files "restrt" (in addition to trajectory files) in NetCDF format
and this option is also recommended in the manual. While I'm able to load
Amber NetCDF trajectories (.nc extension) correctly into VMD, it seems that
it's still not possible to load NetCDF restart files. Maybe this has
something to deal with the NetCDF plugin?

I think it can be something related to the fact that in Amber NetCDF
restart files there is no frame dimension, as I can read in VMD when I load
one of those files:

vmd > netcdfplugin) conventions: 'AMBERRESTART'
netcdfplugin) trajectory follows AMBER conventions version '1.0'
netcdfplugin) AMBER: program 'pmemd'
netcdfplugin) AMBER: program version '11.0'
netcdfplugin) AMBER: title 'default_name'
netcdfplugin) AMBER: application 'AMBER'
netcdfplugin) AMBER: spatial dimension: 3
netcdfplugin) AMBER: atom dimension: 16757
netcdfplugin) AMBER: missing frame dimension, aborting
netcdfplugin) Missing or unrecognized conventions attribute

Do you have some idea how to solve this, maybe modifying the NetCDF plugin
to handle this file correctly?

Thank you for your attention.

============================================
*Giuseppe La Rosa*, *PhD student*
Technische Universität München
Theoretical Biophysics (T38),
Department of Molecular Dynamics (Prof. Zacharias)
Physics I Garching EG, Room 2701
<https://portal.mytum.de/displayRoomMap?roomid=2701@5101&disable_decoration=yes>
James-Franck-Str. 1
85748 Garching
Germany
Tel: (+49) 89 289 12564
e-mail: giuseppe.la.rosa_at_tum.de
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