Distributions, selection fixed-effects analysis

In addition it is now time to think about the two assumption models, or types of analysis of variance. ANOVA type 1 assumes that all levels of the factors are included in the analysis and are fixed (fixed effect model). Then the analysis is essentially interested in comparing mean values, i.e. to test the significance of an effect. ANOVA type 2 assumes that the included levels of the factors are selected at random from the distribution of levels (random effect model). Here the final aim is to estimate the variance components, i.e. the variance fractions with respect to total variance caused by the samples taken or the measurements made. In that case one is well advised to ensure balanced designs, i.e. equally occupied cells in the above scheme, because only then is the estimation process straightforward. 

Minimization and vibrational analysis are useful for the determination of force field parameters, system preparation, and the study of many problems of biological interest. A new optimizer based on a truncated Newton method (TNPACK) that is effective for large molecules has been added to CHARMM. All minimizers, excluding TNPACK, support the use of holonomic constraints on selected bonds and angles (SHAKE). Vibrational analysis has been extended via addition of the MOLVIB module (K. Kuczera and J. Wiorkiewicz-Kuczera, unpublished), which allows for the determination of potential energy distributions and the analysis of lattice modes in combination with the CRYSTAL facility. Minimizations may also be performed in the presence of a variety of structural constraints. This allows for atomic positions, internal coordinates, interatomic distances, etc. to be fixed or constrained to specified values. Such constraint methods may be used in molecular dynamics simulations. 

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