Force-field development

Eorce fields give the best results for m oleciiles similar to those used to develop its parameters. Choose a force field developed for a range of molecules similar to your molecular system. 

Wofe." rh c BIO + force field is an im plern en lation oflheCH. ARMM (Chcmistry at H.ARvard MacromoIceular Mechanics ) force field developed in the group of Martin Karplusat Harvard University, l.ike. AMBER and OP1.S, it is primarily designed to explore rnacro-moleciilcs. 

The AMBER (Assisted Model Building and Energy Refin emeni) is based on a force field developed for protein and nucleic acid computations by members of the Peter Kollman research group at the... 

OPTS (Optim i/.ed Potentials for Liquid Simulations) is based on a force field developed by the research group of Bill Jorgensen now at Yale University and previously at Purdue University. Like AMBER, the OPLS force field is designed for calculations on proteins an d nucleic acids. It in troduces non bonded in leraclion parameters that have been carefully developed from extensive Monte Carlo liquid sim u lation s of small molecules. These n on-bonded interactions have been added to the bonding interactions of AMBER to produce a new force field that is expected to be better than AMBER at describing simulations w here the solvent isexplic-... 

AMBER, BIO-h and OPLS scale 1 van der Waals and 1 electrostatic interactions. Although the value of the 1 nonbonded scale factors is an option in HyperChem, you should generally use recommended values. This is because during parameterization, the force field developers used particular values for the 1 nonbonded scale factors, and their parameters may not be correct for other scale factors. 

Note All of the force fields provided in HyperChem are built on new implementations of force fields developed by various computational chemistry research groups. However, HyperChem improves on the original force fields and uses new code. 

Such results are interesting for force field development as they clearly establish the existence of conserved electrostatic blocks within amino acids, an encouraging step for transferability of force field parameters. 

F. -Y. Dupradeau, and J. Kovensky, Multi-mannosides based on a carbohydrate scaffold Synthesis, force field development, molecular dynamics studies, and binding affinities for lectin Con A, J. Org. Chem., 72 (2007) 9032-9045. 

Molecular Mechanics Force Field Development and Applications... 

BIOGRAF supports a number of force fields (AMBER, MM2, and DREIDING). The DREIDING force field, developed for the BIOGRAF... 

SYBYL. A Molecular Mechanics Force Field developed by Tripos, Inc. 

It is worth a pause, however, to consider how such models should best be used. Part of the motivation for developing linear scaling models has been to permit QM calculations to be carried out on biomolecules, e.g., proteins or polyiiucleic acids. However, one may legitimately ask whether there is any point in such a calculation, beyond demonstrating that it can be done. Because of the relatively poor fashion with which semiempirical models handle non-bonded interactions, there is every reason to expect that such models would be disastrously bad at predicting biomolecular geometries - or at the very least inferior to the far more efficient force fields developed and optimized for this exact purpose. 

We now consider separately each function used to calculate the terms that go to make up the total strain energy. We have restricted our discussion here to the simplest forms of the functions. With the greater approximations involved in modeling metal complexes, refinements of the functions are often an unneccessary elaboration. A full account of possible functions is given in Chapter 2, Section 2.2. When the use of other functions is indicated, these can be parameterized by application of the general philosophies of force field development outlined below. 

Thompson, M. A. (1995), Hybrid QM/MM Molecular Force Field Development for Large Flexible Molecules a MD study of 18-crown-6, J. Phys. Chem. 99, 4794-4804. 

K. D. Gibson and H. A. Scheraga. Decisions in force field development. Reply toKollmain and Dill. J. BtomoL Struct. Dyn. 1109-1111 (1991). 

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