Compiler version and regression tests
If recommended software are not used for compilation, warning messages might be displayed in the terminal when the
configure command is executed. That message is just a warning, not an error. So you can continue the compilation. However, we strongly recommended you to perform regression tests to check whether GENESIS is properly working.
What are installed to bindir?
make install” command generates all executables and then copy them into the
bin directory. The
bin directory is created at the same level as the
src directory. Files in the
bin directory of GENESIS 1.1.x may look like this:
$ cd ../bin $ ls atdyn eigmat_analysis pcrd_convert remd_convert spdyn avecrd_analysis flccrd_analysis prjcrd_analysis rmsd_analysis trj_analysis mbar_analysis prst_setup rst_convert wham_analysis crd_convert qval_analysis rst_upgrade
spdyn are the MD programs. Other executables are builder, modeler, converter, and trajectory analysis tools. For example,
trj_analysis analyzes distance, angle, and dihedral angles, and
rmsd_analysis calculates root-mean-square deviation (RMSD) of the selected atoms in the trajectory data.
If you add
./configure, only spdyn will be installed.
If you wanna fully recompile GENESIS, following commands will work.
$ make clean $ make distclean $ ./configure $ make $ make install
Note that the direct
make clean command may not work in the case where Makefiles were created in another machine. In this case, the user should run the
./configure command before
When you modified configuration files (configure.ac, Makefile.am)
If you modified
Makefile.am by yourself and met an error during compilation, you may need to run the “
bootstrap” script in the
src directory before