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JavaGenes: Evolving Molecular Force Field Parameters

Al Globus*, a, Charles Bauschlicherb, Sandra Johanb, and Deepak Srivastavaa

aCSC at NASA Ames Research Center, Moffett Field, CA 94035 USA
bNASA Ames Research Center

This is an abstract for a presentation given at the
Ninth Foresight Conference on Molecular Nanotechnology.
There will be a link from here to the full article when it is available on the web.


Accurate molecular dynamics simulation of reactive multi-species systems is important to the design of artificial molecular machines. For example, the existing reactive hydrocarbon Brenner's potential has been used to design gears, hinges, three-way junctions, and bearings and helped motivate the design of a hydrocarbon assembler. Unfortunately, reactive multi-species potentials are only available for C-H-nobel gas, Si-F, Si-C-Ge and a few others. This is not sufficient to design molecular factories of the type envisioned by Drexler. Furthermore, developing reactive multi-species potentials is difficult, time consuming, tedious, failure prone and, thus, rarely attempted.

There are two parts to developing any force field: finding a functional form that reflects the physics and choosing the parameters required by the form. Much of the tedium is in the parameterization. We hypothesize that this step can be automated by large computations on cycle-harvested desktop computers. By automating parameterization, exploration of functional forms should be enhanced.

Given a functional form, the parameters are typically chosen to fit experimental values and/or ab initio calculations. The fitting process can be difficult because functional forms usually have many local minima that tend to trap search algorithms. We are developing the JavaGenes genetic algorithm to evolve force field parameters. Genetic algorithms are somewhat less likely to fall into local minima than simulated annealing or hill climbing. For proof of concept, we have evolved the (Stillinger and Weber 90) published parameters for Si and F separately with good, although not yet perfect, results. Over the next few months we expect to evolve the full, combined Si-F published parameters and compare the results with parameters fitted to ab initio energy calculations.


Table 1 shows results evolving the (Stillinger and Weber 90) Si parameters: For two body parameters we fit the energies of 100 Si dimers spaced 0.5-3.7 angstroms apart. The three body parameters were evolved separately with the two body parameters fixed to the best values from the two-body run and fit to 400 Si tetrahedra randomized around the low energy conformation.

Table 1
Parameter Published value Evolved value
A 7.049556277 7.062138589233899
B 0.6022245584 0.6283594386627
C 1.0 0.9999066666678916
p 4.0 3.9970443831775535
q 0.0 0.005038128110635121
Three body parameters
alpha 0.0 -0.00476705603392214
lambda 21.0 21.030398353724657
gamma 1.2 1.2003753288365615

Table 2 shows results evolving the (Stillinger and Weber 90) F parameters. For two body parameters we fit the energies of 100 F dimers spaced 0.5-5 angstroms apart. The three body parameters were evolved separately with the two body parameters fixed and fit to 100 F2+F confomations.

Table 2
Parameter Published value Evolved Value
A 0.52276 0.536060720470749
B 0.11277 0.123804003816043856
C 0.579495 0.5794579857222181
p 8.0 7.884508889552029
q 4.0 4.055374744348555
Three body parameters
alpha 38.295 31.904841586417522
lambda -19.1475 -23.848659093495885
gamma 1.738485 1.84226440597913
delta 0.0818182 6.711483050303828
m 4.0 2.2224104136309757
beta 0.579495 2.4738447463466304

Note: The functional form was transformed to give all terms an identical form, except FFF where the last three parameters are unique. These three parameters have not yet been accurately evolved by JavaGenes. Once the proof of concept is complete, we will use the procedures developed to create reactive force fields for new systems, e.g., BN nanotubes.


(Stillinger and Weber 90) Frank H. Stillinger and Thomas A. Weber, Dynamical Branching during Fluorination of the Dimerized Si(100) Surface: A Molecular Dynamic Study, Journal of Chemical Physics, 92(10), pages 6239-6245, 15 May 1990.

*Corresponding Address:
Al Globus
CSC at NASA Ames Research Center
T27A-1, NASA Ames, Moffett Field, CA 94035 USA
phone: (831) 464-8404


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