Source code that I have used in various projects...
1. A ___Molecular Dynamics___ program capable of simulating mixtures of various chain molecules of the form -(AXY-Bm)n where A and B are backbone atoms and X, Y are substituents. It is an offspring of an older program developed by ___prof. D. N. Theodorou___ and his coworkers; I have made numerous modifications and additions to meet my needs.  
2. A ___Molecular Mechanics___ program that can build bulk systems of linear molecules of various molecular weights (united atom approximation). 
3. A ___Bulk System Energy Optimization___ program, complementig the previous one. It decreases the energy and relaxes the structure of the systems generated by the Molecular Mechanics software, thus generating a more representative sample. A simple Monte Carlo scheme is employed instead of local algorithms, to better explore the configurational space. 
4. A ___program___ to calculate pair distribution functions of bulk polymer systems and other geometric quantities of interest, using trajectories obtained via MD or MC. 
5. Another ___program___ calculating diffusion coefficients by means of the well-known Einstein relation. It also generates information regarding anisotropy of diffusion. This is especially useful in studying motion of small penetrants travelling through slowly moving or completely fixed matrices like polymers or zeolites. 
6. Velocity autocorrelation functions can be computed by ___this program___ if one wants to apply the Green-Kubo relations.  
7. Time correlation functions of subchain end-to-end vector orientation and of dihedral angles are calculated ___here___ in order to obtain information about geometrical relaxation of polymer systems throughout simulation runs and relevant time scales. 
8. Another program developed by ___prof. D. N. Theodorou's___ coworkers and subsequently modified by me: ___It calculates___ chemical potential solubility coefficients of short chain molecules inserted in a given matrix (Widom insertion method). A reference value is needed for the chemical potential and it is calculated by ___this program___. 
9. Various versions of a ___program___ calculating force-field parameters for a given molecule of the -(AXY-Bm)n type  (see Nr 1 in this list), based on quantum mechanically optimized geometries and their energies. 
10. Various versions of a ___program___ minimizing the force-field energy of a single molecule of the -(AXY-Bm)n type  (see Nr 1 in this list); it is used as a tool complementing the previous program in order to develop new ab initio based force fields. 
11. More software will be uploaded, hopefully soon, including programs to calculate various thermodynamic quantities of simulated systems, a single chain Monte Carlo code and a new method to detect jumps performed by penetrants travelling through slowly moving or fixed matrices, and treat them quantitatively.  

I apologize for the messy code and lack of documentation, due to my limited time. Should you be interested, feel free to ___contact me___.