[gmx-users] Re: Gromacs analysis tools for Namd output
francesco.oteri at gmail.com
Tue Feb 7 21:19:36 CET 2012
it is possible the dl library (containing the function to dinamically
loading libraries) is missed.
To confirm this hypotesis, try:
On my PC this is the output:
linux-vdso.so.1 => (0x00007fffdddd6000)
libgmxana.so.6 => /apps/gromacs/4.5.5/gnu/lib/libgmxana.so.6
libmd.so.6 => /apps/gromacs/4.5.5/gnu/lib/libmd.so.6
libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007f6e501a9000)
libgmx.so.6 => /apps/gromacs/4.5.5/gnu/lib/libgmx.so.6
* libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6e4f542000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6e4ef8f000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6e4ed77000)
If you miss this library, try to instrall again gromacs including this
Il 07/02/2012 20:04, Kunze, Micha ha scritto:
> Hey Paul,
> cant help you with the plugin issue, but have you instead tried
> loading the dcd trajectory into vmd and save it as trr?
> On 7 Feb 2012, at 18:18, "PAUL NEWMAN" <paulclizana at gmail.com
> <mailto:paulclizana at gmail.com>> wrote:
>> Dear Gromacs users,
>> This is my second email since I tried the previous advises and did
>> NOT work.
>> I want to use the Gromacs analysis tools for analyzing Namd output
>> files (*.dcd files) I installed Gromacs 4.5.4 (64 bits) and it works
>> well. In addition I installed VMD 1.9 (64 bits) 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*
>> Can anyone tell me if Gromacs really works with the VMD pulgin?
>> I will highly appreciate to know it so I can start looking for
>> another alternatives.
>> Thanks so much
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