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

qiaobf qiaobf at gmail.com
Mon Jul 28 23:27:25 CEST 2014

Hi All,

One update: The first problem regarding the math library has been solved 
by changed:
> target_link_libraries(g_density2 ${GROMACS_LIBRARIES})
> target_link_libraries(g_density2 ${GROMACS_LIBRARIES}*m*)

However, the 2nd problem regarding displaying the INSTRUCTION text has 
not solved. Any one can help? Thanks a lot!
> qiaobf at NU:~/programmes/GROMACS-5.0/bin/QiaoBF$ g_density2 -h
> -------------------------------------------------------
> Program GROMACS, VERSION 5.0
> Source code file: 
> /home/qiaobf/programmes/backup/gromacs-5.0/src/gromacs/commandline/pargs.cpp, 
> line: 874
> Invalid command line argument:
> -h
> For more information and tips for troubleshooting, please check the 
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------


On 07/28/2014 11:05 AM, qiaobf wrote:
> Dear Mark,
> Thanks a lot for your kind help. I have corrected the linkages to the 
> heading files. However, I got a few more problems:
> 1)  The math library is not recognized when compiling. See below for 
> the error message. Is there a way to add the flag of "-lm" under 
> cmake? For instance, "gcc test.c -lm -o test" works where sqrt is also 
> used.
>> undefined reference to symbol 'sqrt@@GLIBC_2.2.5'
> 2) If the line with "sqrt" function is commented out, the g_density2 
> can be successfully generated. however, the "./g_density2 -h" is not 
> working to display the help contents. Could you please give me some 
> suggestions?
> I am looking forward to your kind help, and appreciate your time!
> best regards,
> Baofu
> On 07/24/2014 04:47 PM, qiaobf 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!
>> 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
>> best wishes,
>> Baofu

Baofu Qiao
Department of Materials Science and Engineering,
Northwestern University
Tel: 224-420-1019
Email: qiaobf at gmail.com

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