Internet Links of Interest
http://www.netsci.org/Resources/Software/Modeling/Biop/: A web page with a list of links to various sites with models for biopolymers.
Biomer: a Java-based, on-line biomolecular modeling package useful for constructing structures for biopolymers and organic molecules. It reads and writes PDB files and performs structure optimization and dynamics via the AMBER force field and steepest descent and conjugate gradient optimization methods. It can export images in a variety of graphical formats including jpeg, gif and ppm. The program is available for free download, and should not be platform dependent as long as your machines has a decent version of Java. Online documentations and examples are available.
DL_POLY from CCP5: a parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith and T.R. Forester. This is a program for classical simulation of condensed phases, available free for noncommercial academic research.
Jean Frechet's Home Page: a page covering the research of Professor Frechet at UC Berkeley, with a description of his research, which is mostly focused on design and synthesis of macromolecules with controlled shape, functionality, and reactivity (lots of interest to those interested in dendritic polymers). Lists of publications and patents are provided
LAMMPS (large-scale atomic/molecular massively parallel simulator): A new parallel molecular dynamics code, suitable for modeling large molecular systems, developed in collaboration between Sandia and Lawrence Livermore National Labs, Bristol-Myers-Squibb, Cray Research, and Dupont. The code computes two kinds of forces: short-range (e.g., van der Waals interactions and molecular bond stretching/bending/torsion) and long-range (Coulombic effects).
MDCM Molecular Dynamics Chain Molecules: simulates an arbitary number of chain molecules of arbitary length on the Paragon parallel computer. Neighboring atoms on a chain molecule are joined by a simple harmonic potential or a finite extensible potential. Intermolecular interaction is a Lennard-Jones potential. Developed by S. T. Cui, P. T. Cummings, and H. D. Cochran.
MesoDyn: a page dedicated to the MesoDyn project -- an effort disseminating information on new developments in mesoscale modeling theory. The site contains some nice overviews and a selection of papers on the topic downloadable in postscript. NOTE: Source code is now available for a 3D phase prediction code for copolymer melts for free download! Sample inputs and outputs are also provided.
Molecular-Based Study of Fluids and Amorphous Materials Using Parallel Supercomputers: a Web site providing information about the ORNL effort in this simulation area. The main attraction of this site is a list of codes developed as part of this work. The codes are not available for download, but contact information is provided for those who might wish to inquire into thei availability. The list includes non-equilibrium molecular dynamics codes for a variety of different systems, constraint dynamics, codes for liquid crystals and chain molecules, as well as novel domain decomposition schemes.
Molecular Simulations Inc.: extensive suite of programs for performing a diverse selection of different computational chemical analyses, from ab initio, to DFT and molecular mechanics. Force field library available for polymer modelling.
http://web.mit.edu/armstronggroup/ Polymer Molecular Theory and Fluid Mechanics,
Multiscale Process Modeling