VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 13 2014 - 11:43:28 CST

Hi,
  I haven't significantly changed the VMD netcdf plugin since
AMBER 9/10 first began supporting NetCDF. I just googled for
their format spec and it does look like they have indeed updated
it as part of their AMBER 13/14 development:
  http://ambermd.org/netcdf/nctraj.xhtml

Since I hadn't heard of this change before now (I wish we'd get
some warning from the AMBER developers about these sorts of changes),
I'll have to read their updated format spec and see how easy it is to
add support for their restart format.

If you can provide some example AMBER 14 restart files, that would be
very helpful. If they are small you can email them to me directly,
if they are large then it would be best if you can post them somewhere
where I can download them.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 07, 2014 at 02:51:26PM +0100, Giuseppe La Rosa wrote:
> 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 UniversitACURt MA 1/4nchen
> Theoretical Biophysics (T38),
> Department of Molecular Dynamics (Prof. Zacharias)
> Physics I Garching EG, Room [1]2701
> James-Franck-Str. 1
> 85748 Garching
> Germany
> Tel: (+49) 89 289 12564
> e-mail: [2]giuseppe.la.rosa_at_tum.de
> ============================================
>
> References
>
> Visible links
> 1. https://portal.mytum.de/displayRoomMap?roomid=2701@5101&disable_decoration=yes
> 2. mailto:giuseppe.la.rosa_at_tum.de 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/