[gmx-users] How to read in netcdf with GROMACS?

a a patd_2 at hotmail.com
Sat May 26 18:37:52 CEST 2012

Dear Sir/Madam,

I am trying to do the following analysis with GROMACS:

/usr/local/gromacs/bin/g_covar -s my.pdb -f my.netcdf -o -v

However, I found the following error message:

GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.
This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.

VMD_PLUGIN_PATH not set. Using default location:

Could not open any VMD library.
Last error:
/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xyzplugin.so: wrong ELF class: ELFCLASS64

Program g_covar, VERSION 4.5.5
Source code file: trxio.c, line: 870

Fatal error:
Not supported in read_first_frame: D1_md7to23.netcdf
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

However, when I double check my /usr/local/lib/vmd/plugins/LINUXAMD64/molfile directory, I can see netcdfplugin.so file.

Why the file cannot recognize to use netcdfplugin.so file to read my.netcdf file, but instead trying to use the xyzplugin.so file?

I have also set the following path in .bashrc file already.

Did I do anything wrong?

Best regards,


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