building plumed with vmd plugins

[qingh...@gmail.com]

Hello,

As I want to ask plumed (driver) to process amber NetCDF trajectory files directly, I tried to install PLUMED with vmd plugin.

As suggested by the Manual, I firstly downloaded the source code of vmd-1.9.3, and there is a  plugins directory.
I built the plugins successfully (tcl 8.5 was also built), and got libmolfile_plugin.a and libmolfile_plugin.h. Then I tried to build PLUMED like this:

./configure --prefix=/path of plumed/plumed233 LDFLAGS="-ltcl8.5 -L/path/vmd1.9.3/plugins/compile/lib_LINUXAMD64/molfile -L/path/vmd1.9.3/plugins/compile/lib_LINUXAMD64/tcl/" CPPFLAGS="-I/path/vmd1.9.3/plugins/compile/lib_LINUXAMD64/molfile/

But libmolfile_plugin.h was not found during the configuration. Could someone give me some tips? Thanks a lot!


All the best,
Qinghua

PS: some notes from the Manual:


VMD trajectory plugins

If you configure PLUMED with VMD's plugins you will be able to read many more trajectory formats. To this aim, you need to download the SOURCE of VMD, which contains a plugins directory. Adapt build.sh and compile it. At the end, you should get the molfile plugins compiled as a static library libmolfile_plugin.a. Locate said file and libmolfile_plugin.h, and customize the configure command with something along the lines of:

./configure LDFLAGS="-ltcl8.5 -L/mypathtomolfilelibrary/ -L/mypathtotcl" CPPFLAGS="-I/mypathtolibmolfile_plugin.h/"

[Giovanni Bussi]

Hi,

I think there is an error in the instructions.

Can you try something like this?

./configure --prefix=/path of plumed/plumed233 LDFLAGS="-L/path/vmd1.9.3/plugins/compile/lib_LINUXAMD64/molfile" CPPFLAGS="-I/path/vmd1.9.3/plugins/compile/lib_LINUXAMD64/molfile/ -I/path/vmd1.9.3/plugins/compile/include"

Notice that I:

- removed tcl related stuff (it's not necessary on my Mac, though you might have to add it back on your system)

- added -I....include to CPPFLAGS . This is required to find the libmolfile_plugin.h file

Let us know if this solves your problem.

Giovanni

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[qingh...@gmail.com]

Dear Giovanni,

Thanks very much for your instruction! It works as you suggested:

./configure --prefix=/path of plumed/plumed233 LDFLAGS="-L/path/vmd1.9.3/

plugins/compile/lib_LINUXAMD64/molfile" CPPFLAGS="-I/path/vmd1.9.3/plugins/compile/lib_LINUXAMD64/molfile/ -I/path/vmd1.9.3/plugins/include"

The include directory is under plugins, but not compile. After making this correction, then the compilation was successful. Thanks!


All the best,
Qinghua

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[Giovanni Bussi]

Thanks! I'll update the manual

Giovanni

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[qingh...@gmail.com]

Thank you, too! :-)

Best,
Qinghua

[qinghua Liao]

Hello Giovanni,

I installed plumed with vmd plugins successfully, but I just found that there is no flag for reading AMBER netcdf trajectory file (*nc).
This is wired, as I can see the other newly added options. The plugins I installed are from the source code of vmd-1.9.3.
I am wondering why the option for AMBER netcdf is missing. What do you think the reason might be? Thanks a lot!


All the best,
Qinghua

On Friday, November 3, 2017 at 12:24:09 PM UTC+1, Giovanni Bussi wrote:

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[Giovanni Bussi]

Hi,

I don't know... Perhaps you should check if when compiling the vmd-plugins the netcdf library is properly found and linked.

If you look in plugins/Make-arch there are, for some machines, hard coded flags such as "-lnetcdf"

Actually, I have no experience with this, sorry...

Giovanni

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[qingh...@gmail.com]

Dear Giovanni,

Thanks a lot for your suggestion! I will then look into it and try to solve it.


All the best,
Qinghua

[qingh...@gmail.com]

In case someone also has the problem, actually I gave up for the installation of plumed with vmd plugin.
But I found a alternative way to do it, I found that the netcdf trajectory file can be converted into xtc format with cpptraj of Amber.
Then, the xtc file can be processed  by plumed.

All the best,
Qinghua