[gmx-users] Gromacs analysis tools for Namd output

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 1 22:47:51 CET 2012

On 2/02/2012 4:35 AM, PAUL NEWMAN wrote:
> Dear Gromacs users,
> I want to use the Gromacs analysis tools for analyzing Namd output 
> files (*.dcd files) I just installed Gromacs 4.5.4 and it works well. 
> In addition I installed VMD 1.9 and set up 
> VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/   (Here it 
> is located the  dcdplugin.so )
> I verified that VMD_PLUGIN_PATH is pointing out to the right folder. 
> However when I run for example
> g_rmsf_d -f file.dcd  -s file.pdb
> I got the following error
> The file format of file.dcd is not a known trajectory format to 
> GROMACS. Please make sure that the file is a trajectory!
> 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.
> No plugin for dcd found
> Am I doing something wrong? Do I need to do something else?
> Any help and advise will be highly appreciate it

Maybe your GROMACS is 32bit and your VMD is 64bit. These would have to 


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