Force fields origin

Following the introdnction of a directional hydrogen bonding potential function into MM3, the parameterization of the force field for the ammonia dimer was undertaken anew . Three conformers were considered, namely 28, 29 and a bifurcated structure 31, and were calcnlated ab initio at the 6-31G level. The results (after corrections for Basis Set Superimposition Error BSSE) favor the linear dimer over the cyclic one by 0.4 kcalmol and yield dimerization energies of —2.49, —2.09 and —0.62 kcalmol for 28, 29 and 31, respectively. A comparison of force field (original MM3 and MM3 with the directional hydrogen bonding function) and ab initio resnlts for the three ammonia... 

Up to now we have considered the case where the force field originates firom two point charges and we have always used the separability for the connections. For the application to molecules we are also interested in the case where... 

In the case shown in Figure 2a the chemical potential of the film, psxj, is the same as that in the 3D film phase under the same conditions. On the other hand, in the case where there are overlapping force fields originating from the two interfrices of the thin film (cf. Figure 2b), the chemical potential deviates from its value in the 3D phase. More precisely. 

To redefine an atom type associated with a force field, adpist the rules in th e ch cm, ru 1 file to represent the new ehernical environment for a particular type and then compile the new types. It is always desirable to save the origin a I eh cm. nil un dcr an oth cr n am c prior to modifying chem.rul. Having modified chem. nil, you can... 

Note All of the force fields provided in HyperChem are built on new irn picm en tatiori s of foree fields developed by various com pii-tational chemistry research groups. How-ever, HyperChem improves on the original force fields and uses new code. 

I tie Hypci Cticm OPI.S force field gives results equivalent to the original OPLS force field. 

Chemistry at Harvard macromolecular mechanics (CHARMM) is the name of both a force field and a program incorporating that force field. The academic version of this program is designated CHARMM and the commercial version is called CHARMm. It was originally devised for proteins and nucleic acids. It has... 

MMl, MM2, MM3, and MM4 are general-purpose organic force fields. There have been many variants of the original methods, particularly MM2. MMl is seldom used since the newer versions show measurable improvements. The MM3 method is probably one of the most accurate ways of modeling hydrocarbons. At the time of this book s publication, the MM4 method was still too new to allow any broad generalization about the results. However, the initial published results are encouraging. These are some of the most widely used force fields due to the accuracy of representation of organic molecules. MMX and MM+ are variations on MM2. These force fields use five to six valence terms, one of which is an electrostatic term and one to nine cross terms. 

The Merck molecular force field (MMFF) is one of the more recently published force fields in the literature. It is a general-purpose method, particularly popular for organic molecules. MMFF94 was originally intended for molecular dynamics simulations, but has also seen much use for geometry optimization. It uses five valence terms, one of which is an electrostatic term, and one cross tenn. 

MOMEC is a force field for describing transition metal coordination compounds. It was originally parameterized to use four valence terms, but not an electrostatic term. The metal-ligand interactions consist of a bond-stretch term only. The coordination sphere is maintained by nonbond interactions between ligands. MOMEC generally works reasonably well for octahedrally coordinated compounds. 

Understanding how the force field was originally parameterized will aid in knowing how to create new parameters consistent with that force field. The original parameterization of a force field is, in essence, a massive curve fit of many parameters from different compounds in order to obtain the lowest standard deviation between computed and experimental results for the entire set of molecules. In some simple cases, this is done by using the average of the values from the experimental results. More often, this is a very complex iterative process. 

The force fields available are MM2, MM3, AMBER, OPLSA, AMBER94, and MMFF. The asterisk ( ) indicates force fields that use a modification of the original description in the literature. There is support for user-defined metal atoms, but not many metals are predefined. MM2 has atom types for describing transition structures. The user can designate a substructure for energy computation. 

University of California, San Francisco. The original AMBER has become one of the more widely used academic force fields and extensive work has gone into developing it — resulting in a number of versions of the method and associated parameters. Hyper-Chem gives results equivalent to Versions 2.0 and 3.0a of the AMBERprogram distributed by the Kollman group and parameter sets for both these versions are distributed with HyperChem. 

HyperChem uses the improper dihedral angle formed by central atom - neighbor 1 - neighbor 2 - neighbor 3, where the order of neighbors is how they appear in a HIN file. Not all planar atoms customarily have associated improper torsions. The order of atoms is arbitrary but has been consistently chosen by the original authors of the CHARMM force field. The templates contain equivalent CHARMM definitions of improper torsions for amino acids. Improper dihedral angles cannot be defined that do not have a central atom, as is sometimes done in CHARMM calculations. 

Deposition Origin of force field Basic parameter Specific modifying parameters System parameters... 

The original molecular-mechanics force field was developed by Allinger, and is generally referred to as MM. You should read the definitive text by Burkert and Allinger (1982) for more details. This model was followed by the MM2 model (Allinger, 1977), and I thought that you might like to read the synopsis. 

This force field was developed primarily for protein and nucleic acid applications. It is a united atom force field, and there are many versions. Once again, you might like to see the Abstract of the original Paper. 

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