Installation Notices

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?

The “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

Atdyn and 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 --enable-single to ./configure, only spdyn will be installed.

Clean installation

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 make clean.

When you modified configuration files (,

If you modified or by yourself and met an error during compilation, you may need to run the “bootstrap” script in the src directory before ./configure and make.