![]() ![]() The script must have the “executable” attribute, set via “chmod +x installer-file-name.sh”, prior to being run. The Tinker-FFE Installer for Linux is provided as a gzipped shell script. Several other visualization programs (including VMD, Avogadro, Jmol, MOLDEN, WebMO, some PyMOL versions, etc.) can display Tinker structure and MD trajectory files. For research work, we recommend using the latest command line version of Tinker for numerical calculations, and using FFE or another visualization program to view results. Integration with Tinker, including the ability to interactively run Tinker calculations, and to access molecule downloads from the PubChem, NCI and PDB databases make Tinker-FFE a useful tool in classroom teaching environments. Tinker-FFE requires a 64-bit CPU and operating system, as 32-bit systems are no longer supported. Tinker-FFE for Linux, MacOS and Windows can be downloaded from the Ponder lab Tinker web site as “installation kits” containing the FFE GUI and an FFE-enabled version of Tinker. It provides visualization for Tinker molecule files, as well as launching of Tinker calculations from a graphical interface. Tinker-FFE, formerly Force Field Explorer, is a Java-based GUI for the Tinker package. A description of the other parameter values is contained in the header of the file. Personal computers with minimal memory may need a lower limit, depending on available memory, swap space and other resources. This parameter can be set to 1000000 or more on most workstations. The basic limit is on the number of atoms allowed, “maxatm”. The most common source alterations are to the master array dimensions found in the source file sizes.f. Regardless of your target machine, only a few small pieces of code can possibly require attention prior to building. Sample compgui.make and linkgui.make scripts are provided for systems capable of building GUI-enabled executables. Then executables must be linked against Java libraries in addition to the usual resources. Building FFE-enabled Tinker executables involves replacing the sockets.f source file with sockets.c, and included the object from the C code in the Tinker object library. These steps will produce executables that can run from the command line, but without the capability to interact with the FFE GUI. The executables can be renamed and moved to wherever you like by editing and running the “rename” script. Finally, run a link.make script to produce the complete set of Tinker executables. Next you must use a library.make script to create an archive of object code modules. The first step in building Tinker using the script files is to run the appropriate compile.make script for your operating system and compiler version. As an alternative to Makefiles, we also provide machine-specific directories with three separate shell scripts to compile the source, build an object library, and link binary executables. ![]() We provide in the /make area of the distribution a Makefile that with minor modification can be used to build Tinker on any of these machines. The compilation and building of the Tinker executables should be easy for most of the common Linux, MacOS and Windows computers. ![]()
0 Comments
Leave a Reply.AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |