VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Dec 19 2019 - 03:46:08 CST

Well, the only thing I can say at this point is that vmd 1.9.4a12 reads
the trajectories perfectly, whereas vmd 1.9.4a38 does not and gives the
error I reported. First I thought its one trajectory that is corrupted
but then I checked it with other programs and it was fine. After that I
realized that the a38 version of vmd does not ready any other netcdf
trajectory I have ...

Except the VMD version, I have not changed anything to the system ...

I will look further into it and see if I can figure out what is happening.

Best,
Vlad

On 12/18/19 5:19 PM, John Stone wrote:
> Vlad,
> The only change to the NetCDF plugin (since 2016 actually) has been
> to correct a memory leak for a cell angles unit string in the AMBER
> reader code, nothing that would impact the eror you reported:
>
> @@ -133,6 +133,9 @@
> if (cdf->amber.cell_lengths_units)
> free(cdf->amber.cell_lengths_units);
>
> + if (cdf->amber.cell_angles_units)
> + free(cdf->amber.cell_angles_units);
> +
> /* MMTK stuff */
> if (cdf->mmtk.comment)
> free(cdf->mmtk.comment);
> @@ -1121,7 +1124,7 @@
> plugin.prettyname = "NetCDF (AMBER, MMTK)";
> plugin.author = "Konrad Hinsen, John Stone";
> plugin.majorv = 1;
> - plugin.minorv = 1;
> + plugin.minorv = 2;
> plugin.is_reentrant = VMDPLUGIN_THREADSAFE;
> plugin.filename_extension = "nc,ncrst";
> plugin.open_file_read = open_cdf_read;
>
>
> I expect that the problem you're seeing is something deeper in
> the NetCDF library itself.
>
> Best,
> John Stone
>
> On Wed, Dec 18, 2019 at 02:25:11PM +0100, Vlad Cojocaru wrote:
>> Dear all,
>>
>> Did VMD change the netcdf plugin between version 1.9.4a12 and 1.9.4a38 ?
>> I am using netcdf trajectories created with CPPTRAJ program from
>> AmberTools 19.
>>
>> When I load these trajectories in VMD 1.9.4a12, everything works well ....
>>
>> However, with VMD 1.9.4a38, I cannot load exactly the same
>> trajectories loaded correctly with the a12 version. I am getting the
>> error below. I will revert for now to the a12 version, but maybe
>> this is worth investigating.
>>
>> Best wishes
>> Vlad
>>
>> netcdfplugin) conventions: 'AMBER'
>> netcdfplugin) trajectory follows AMBER conventions version '1.0'
>> netcdfplugin) AMBER: program 'cpptraj'
>> netcdfplugin) AMBER: program version 'V18.01'
>> netcdfplugin) AMBER: title 'Cpptraj Generated trajectory'
>> netcdfplugin) AMBER: application 'AMBER'
>> netcdfplugin) AMBER: spatial dimension: 3
>> netcdfplugin) AMBER: atom dimension: 13042
>> netcdfplugin) AMBER: frame dimension: 80000
>> netcdfplugin) AMBER: coordinates units: 'angstrom'
>> netcdfplugin) AMBER: no coordinates scalefactor attribute, 1.0 assumed
>> netcdfplugin) AMBER: coordinates scalefactor: 1.000000
>> netcdfplugin) AMBER trajectory contains periodic cell information
>> netcdfplugin) AMBER: cell lengths units: 'angstrom'
>> netcdfplugin) AMBER: no cell lengths scalefactor attribute, 1.0 assumed
>> netcdfplugin) AMBER: cell lengths scalefactor: 1.000000
>> netcdfplugin) AMBER: cell angles units: 'degree'
>> netcdfplugin) AMBER: no cell angles scalefactor attribute, 1.0 assumed
>> netcdfplugin) AMBER: cell angles scalefactor: 1.000000
>> Info) Using plugin netcdf for coordinates from file ../test.ncdf
>> vmd_LINUXAMD64: putget.c:3593: getNCvx_float_float: Assertion `value
>> != ((void *)0)' failed.
>> Abort (core dumped)
>>
>> --
>> Vlad Cojocaru, PD (Habil.), Ph.D.
>> -----------------------------------------------
>> Project Group Leader
>> Department of Cell and Developmental Biology
>> Max Planck Institute for Molecular Biomedicine
>> Röntgenstrasse 20, 48149 Münster, Germany
>> -----------------------------------------------
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/43241/cojocaru 

-- 
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru