[gmx-users] how to compile and make a C analyzing code under GROMACS 5.0

Mark Abraham mark.j.abraham at gmail.com
Fri Jul 25 00:18:06 CEST 2014

On Thu, Jul 24, 2014 at 11:47 PM, qiaobf <qiaobf at gmail.com> wrote:

> Dear all,
> Please help me out. Thanks in advance.
> I had written some analyzing codes, which can be easily compiled under
> Gromacs 4.5.5. Since I switched to GMX 5.0 weeks ago, I want to re-compile
> them under GMX5.0. But the GMX5.0 seems quite different from GMX4.5.5.
> Anyone can help me? Thanks a lot!
> I have tried the following methods:
> 1)  (a) save the gmx_density2.c under $HOME/programmes/backup/
> gromacs-5.0/src/gromacs/gmxana, which is the folder to save all the
> gmx_XXX.c analyzing codes under the distribution folder;
>      (b) re-install the whole package of GMX5.0 (cmake-->make--->make
> install). I got no error message. All regular analyzing programs are
> correctly installed, but not the gmx_density2!

That's not too surprising. You had to do more than dump a file into
src/tools to get gmx_density2 to build in 4.5.5 ;-) You can probably do
something like the above if you register your module with the new gmx
binary - see

> 2) (a) run "source $HOME/programmes/GROMACS-5.0/bin/GMXRC";
>     (b) save the gmx_density2.c under $HOME/programmes/GROMACS-5.0/share/gromacs/template,
> which is under the executable folder;
>     (c) modify the content of CMakeList.txt to change "template" to
> "gmx_density2", and "template.cpp" to "gmx_density2.c";
>     (d) run "cmake .". No error message, and the Makefile and the folder
> CMakeFiles are created;
>     (e) run "make". Then I get the error message
>> gmx_density2.c:42:22: fatal error: sysstuff.h: No such file or directory
>>  #include "sysstuff.h"
>>                       ^
>> compilation terminated.
>> make[2]: *** [CMakeFiles/gmx_density2.dir/gmx_density2.c.o] Error 1
>> make[1]: *** [CMakeFiles/gmx_density2.dir/all] Error 2
>> make: *** [all] Error 2
Things change. You'll need to comment out that #include, see what breaks,
and work out how to include the right header to get the right symbols


> best wishes,
> Baofu
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