Software Downloads
ForceFit and moleculaRnetworks
The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy-to-use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from Gaussian and NWChem. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program.
ForceFit is offered under a LGPL license, wherein the user may not redistribute the code, but modifications may be made and if sent back to Prof. Clark, will be incorporated into the next version of the code.
Any results obtained with ForceFit should refer to the following publication:
Waldher, B.; Kuta, J.; Chen, S.; Henson, N.; Clark, A. E. ForceFit: A Code to Fit Classical Force Fields to Quantum Mechanical Potential Energy Surfaces, J. Comp. Chem. 2010, 31, 2307-2316.
NEW!!! ForceFit Version 2.0
The latest version of ForceFit has been modified to make it easier for the user to fit complex potential functions with many variables. Instead of typing in all terms of the potential within the GUI, the GUI now looks for a template input file for the particular MD algorithm that is to be used, simply designate the variable as #A# or #B#, etc., within the input file and put in the initial parameters within the GUI and you are ready to run.
moleculaRnetworks is a bundled series of scripts, written in the software package R, for processing molecular simulations data. These scripts are intended for the frame-by-frame geometric and solvent network analysis of aqueous solutes, but can be extended to other H-bonded solvents. The algorithms contained therein are based on graph theory and contain a novel method for identifying the geometric shape adopted by the solvent in the immediate vicinity of the solute, as well as an exploratory approach for describing H-bonding, based on the PageRank algorithm implemented by the Google search engine. The moleculaRnetworks codes include a preprocessor which distills simulation trajectories into physicochemical data arrays, and an interactive analysis script that enables statistical, trend, correlation analyses and other data mining. The goals of these scripts is to increase access to the wealth of structural and dynamical information that can be obtained from molecular simulations.
Any results obtained with moleculaRnetworks should refer to the following publication:
Mooney, B. L.; Corrales, L. R.; Clark, A. E. moleculaRnetworks: an Integrated Graph Theoretic and Data Mining Tool to Explore Solvent Organization in Molecular Simulation, J. Comp. Chem., 2012, DOI: 10.1002/jcc.22917, early view.
This paper also has a detailed description of a typical user session and can act as a user manual.
Download moleculaRnetworks
What does Google think about this program?
"Our goal in search is to help people expand their knowledge of the world, and we're delighted to see that our PageRank algorithm is being used to do just that with this innovative and efficient molecular research method," said Amit Singhal, Google Fellow and senior vice president, in an emailed statement.