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VERSION HISTORY

Modelfree version 2.0

Initial public release

Modelfree version 2.1

Bug in simulations of uncertainties fixed.

Modelfree version 3.0 15Jun94 AGP

This is a nearly complete rewrite of the modelfree package. The code is now considerably cleaner and more flexible. The main improvements to the code are noted below.

1. Input file The input file format is now more flexible. In particular, physical constants (gyromagnetic ratio, bond length and chemical shift anisotropy) are input for each spin; thus, spins with different physical properties (13C vs. 15N) can be analyzed simultaneously. In addition, bounding constraints on allowed values of the model free parameters (Sf2, Ss2, te, and Rex) can be set independently for each spin as desired. tm can be optimized independently for each spin if desired (or some spins can be locked to the global tm value and some spins can have independent tm values).
2. Determination of tm The determination of a global value of tm now works better. Under some (difficult to determine) circumstances, the previous versions of the programs were insensitive to small (~0.1 ns) differences in tm values. This problem is now fixed.
3. Monte Carlo simulations In previous vesions of the program, initial guesses for the simulations were taken as the optimized values of the model free parameters. While this seems intuitive, in some cases the resulting optimizations get trapped in undesired local minima. The new code incorportates as an option (see man page), a grid search or simplex search for initial guesses for each simulation. While the resulting code is slower, the simulations are more satisfactory. In particular, the Geary Z value is better behaved (see man page for a discussion).
4. Uncertainties The program now reports uncertainties in the model free parameters from the covariance matrix as well as the Monte Carlo simulations. See Numerical Recipes and the man pages for discussions.
5. Random number generator The seed for the random number generator is now taken from the system clock. If your fortran compiler does not support the function 'time'; then, the routine 'getseed.f' will need to be modified.
6. Statistics Mean, standard deviations and Geary Z values for model free parameters are calculated using trimmed data. That is, the upper and lower x% of the simulated results are discarded prior to the calculation. The value of x is set by the variable 'trim' in modelfree.f. At present the value is 0.10, corresponding to 10% trim. This can be reset by the end user prior to compilation(trim=0 yields raw, untrimmed statistics). Trimming reduces the sensitivity of the simulated results to a small number of outliers.
7. Modelfree output files In addition to the output report, a separate file is produced for each spin called 'title.sim' in which title is the identifier of the spin in the input file. The file title.sim contains SSE and the optimized model free parameters for each simulated data set. Inspection of these files can assist the user in deciding how reliable the simultions are. We normally plot histograms using Kaliedagraph or other plotting program. These files are also useful if you wish to calculate uncertainties in the model free parameters by some other perscription (i.e. untrimmed statistics or absolute deviations etc.)
8. Please see comments in 'Makefile' for modifications you might need to make before compiling

Modelfree version 3.1 1Nov95

1. Rex The programs now properly account for the omega**2 dependence of R(exchange) contributions to R2 when multiple fields are used. The reported Rex results in the output reports are for field_1 in the input field list. Rex results for other fields are given by Rex*(field_n/field_1)**2
2. Modelfree output files The files 'title.sim' have been renamed to 'title.extension' where 'extension' is provided on the command line in the form '-e extension'. If the -e flag is not provided then the files will not be output.
3. Mfgrid output files In addition to the mfout and parmout files, mfgrid will produce a separate file for each spin called 'title.extension' in which 'title' is the identifier of the spin in the input file and 'extension' is provided on the command line in the form '-e extension'. If the -e flag is not provided, then the files will not be output. The file 'title.extension' contains SSE and the grid values of the model free parameters. Inspection of these files can assist the user in deciding how sensitive the model free parameters are to the input relaxation data. We normally plot graphs of SSE versus parameter using Kaliedagraph, Mathematica or other plotting program.
4. -s flag A different model can be fit to the data during the simulations than was used for the fitting. The new model is specified using -s xxxxx where x is 0 or 1, depending on whether a parameter should be included in the model. This option is most useful when performing exploratory runs for model selection. Typically one would analyze the data with tm fixed. If this flag is omitted, then the same model is used for both fitting and simulations.

Modelfree version 4.0 Release date: 15Mar98

The software has been extensively re-written to model overall rotational diffusion using an axially symmetric diffusion tensor. At the same time, the program was modified to improve flexibility in data fitting, statistical analysis, and output format.

1. A separate grid search program (mfgrid in previous versions) does not exist. The grid search functionality has been incorporated into modelfree itself.
2. An axially symmetric rotational diffusion tensor for the molecule of interest is determined by using a simulated annealling or a conjugate gradient algorithm, as desired.
3. Modelfree now allows two different motional models to be specified for each spin. The f statistic is calculated from the fitted results, within a single run of the program.
4. The output file format has been modifed so that the file conforms to the STAR specifications. Particular output information can be extracted from the main output file by using the STAR_BASE program, NAWK, PERL or other text processing utilities

Modelfree version 4.01 Release date: 15Jul98

1. Fixed errors in calculation of F-statistic simulated distribution.
2. Added output of SSE for model 2 in simulation output file (-e flag)
3. Trimmed simulated F-distribution to include only simulations in which an improved SSE is obtained for model 2. The number of simulations used in determining the F-distribution is output as _F-simulations in output file.
4. Fixed output file so an overflow is not obtained for _t-value if _Uncertainty is zero (that is, if zero uncertainty is input for a relaxation datum).

Modelfree version 4.10 Release date: 4Feb00

1. Added uncertainty to csa value for error analysis
2. Added the relaxation interference rate constant ratio eta_xy/eta_z as an optional relaxation parameter
3. Fixed errors in X2 and F simulated distributions.

Modelfree version 4.15 Release date: 10Apr02

1. Fixed errors for IRIX due to type checking
2. Fixed flush-to-zero flag for SGI R12000 chip