Parameters, default

BETA cols 11-20 oscillation control parameter default value is set equal to 0.25. To help prevent oscillations (thus slowing convergence) we not only require that the sum of squares, SSQ, decreases... 

RP cols 31-40 step-back parameter, default value is equal to... 

SET CONTROL PARAMETERS (DEFAULT VALUES ARE OVERWRITTEN BY INPUT DATA IF SPECIFIED)... 

With Dynamics tab active, enter simulation parameters (default settings step interval, 2.0 fs frame interval, 10 fs terminate after 1000 steps, heating/cooling rate, 1.0 kcal/atom/ps and target temperature, 300 K). 

Locate and delete one of each pair of very highly correlated parameters (default r>0.99)... 

Parameter Default value Range of modification Brief description... 

Second card FORMAT(8F10.2), control variables for the regression. This program uses a Newton-Raphson type iteration which is susceptible to convergence problems with poor initial parameter estimates. Therefore, several features are implemented which help control oscillations, prevent divergence, and determine when convergence has been achieved. These features are controlled by the parameters on this card. The default values are the result of considerable experience and are adequate for the majority of situations. However, convergence may be enhanced in some cases with user supplied values. 

PRCG cols 21-30 the maximum allowable change in any of the parameters when LMP = 1, default value is 1000. Limiting the change in the parameters prevents totally unreasonable values from being attained in the first several iterations when poor initial estimates are used. A value of PRCG equal to the magnitude of that anticipated for the parameters is usually appropriate. 

Note MM-i- is derived from the public domain code developed by Dr. Norm an Allinger, referred to as M.M2( 1977), and distributed by the Quantum Chemistry Program Exchange (QCPE). The code for MM-t is not derived from Dr. Allin ger s present version of code, which IS trademarked MM2 . Specifically. QCMPOlO was used as a starting point Ibr HyperChem MM-t code. The code was extensively modified and extended over several years to include molecular dynamics, switching functuins for cubic stretch terms, periodic boundary conditions, superimposed restraints, a default (additional) parameter scheme, and so on. 

A m oleciilar ni echaiiics meih od in HyperChem isdefined by a set of atom types and a functional form for the energy and its derivatives for example. AMHKR. For the. AMBKR method, you may use many different default and iiser-defmed parameter sets. Hyper-... 

The text form for parameters uses white space or commas to separate the fields (columns) of the parameter tiles. They can be read by ordinary text editors, w ord processors, etc. In the text form, param eters are easy to m odify but not easy to com pare, stn dy, etc. Many database program s are capable of reading column s of text as a database, h owever. Wh ile spreadsheets are n ot. per se, databases, they can be useful for examining parameter sets. Microsoft Excel, for example, can read the text form of a param eter file and pn t the data in a form easily manipulated as a matrix or a database. The text form of parameters are stored, by default only, in Tart files. 

Covalen t radii for all th e clem cn ts are readily available an d the bond orders of all bonds arc available from the molecular graph. Prior to describing the explicit default parameter scheme, it is nee-... 

The default parameters for bond stretching are an ec iiilibriiim bond length an d a stretch in g force eon starit. fb e fun etion al form isjiist that of the. M.M+ force field including a correction for cubic stretches. The default force constant depends only on the bond... 

I h e -M. l+ force field assigns default values for out of plane bending terms around an sp2 center. If a central atom has some out of plane parameters, then the first out of plane parameter involving th at cen tral atom is used if a specific parameter is n ot foiin d. 

A diva It MM3 wilh Ihe cumrnand mm3. Answer questions file etheiie.mm3, parameter file Enter (default) line number 1, option 2. The defaull parameter sel is Ihe MM3 parameler sel don t ehange il. The line number starts Ihe system reading on the first line of your input file, and option 2 is the block diagonal followed by full matrix minimi7 ation mentioned at the end of the section on the Hessian matrix. You will see intermediate atomic coordinates as the system minimises the geometry, followed by a final steiic eireigy, Kird with 0, output Enter, cooidinates Enter,... 

Caleulations by the more rigorous proeedure yield, in MM3, a sum of (a) bond energies, (b) steric energy, (c) vibrational zero point and thermal energies, and (d) structural features POP and TORS. Energies (a), (b), and (d) are calculated as before. Bond energy parameters appear to be quite different from those of the default MM3 calculations canied out so far because zero point and thermal energies are not included in the parameters but are added later. 

Try level shifting. This will usually work with the default parameters or not at all. 

Chem comes with default parameter sets, Amber2 and Amber3 in the case of the AMBER method. It is possible, however, to define an arbitrary number of additional parameter sets for the AMBER method (or for any of the other three force field methods). These user-defined parameter sets can be specified in the Parameters dialog box and integrated into HyperChem, in the same way as the default sets. 

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