## ## pyMDMix --- http://mdmix.sourceforge.net ## Software for preparation, analysis and quality control ## of solvent mixtures molecular dynamics ## ## This program is free software; you can redistribute it and/or ## modify it under the terms of the GNU General Public License as ## published by the Free Software Foundation; either version 3 of the ## License, or any later version. ## ## This program is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ## General Public License for more details. ## ## You find a copy of the GNU General Public License in the file ## license.txt along with this program; if not, write to the Free ## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. ## ## Please cite your use of pyMDMix in published work: ## ## TOBEPUBLISHED ## The program is distributed under GNU GPLv3 license. Find the license file under Licenses/ folder. DOCUMENTATION ============= All documentation on program usage is online at http://mdmix.sourceforge.net Installation instructions and usage commands are there explained. Here I will give a brief explanation on installation. INSTALLATION ============ 1- Dependencies --------------- Before installing the program, all dependencies must be fulfilled. As stated in the installation website, most of the dependencies will be automatically installed but these 2: 1) Ambertools. Is the main workhorse where the program has been built upon. 2) Biskit and ScientificPython. Biskit is a python module that manages PDBs very efficiently. Its automatic installation fails and that's why the user has to install it beforehand. Scientific Python which is a dependency of pyMDMix is also a dependency for Biskit. I recommend to install it with NetCDF support. 3) ParmEd 1.1. when working with OpenMM. Once these 3 dependencies are installed, these other list will be automatically installed: - scipy - numpy - matplotlib If they are not, install them manually. 2 - Installation process ------------------------ In main source code folder, type: > python setup.py install This might require admin privileges. You can install a local copy without admin privileges with: > python setup.py install --user 3 - Testing ----------- Test if the python module has been correctly installed: Move to any folder in your system and init a python shell: > python Inside the python shell: >>> import pyMDMix If this loads correctly you should see no error message. Test if the executable user interface has been corectly installed: In any folder type at the shell prompt: > mdmix -h This should print a help message. Test the program works correctly: Move again to the package source directory and type: > python pyMDMix/test.py all This will run a series of source code checks. No test should fail. 4 - Enjoy! ---------- Read program usage at online documentation.