SWITCH_TRACE -- open new optimization trace file

FILE = $\langle{\tt string:1}\rangle$	'default'	partial or complete filename
DIRECTORY = $\langle{\tt string:1}\rangle$	''	directory list (e.g., 'dir1:dir2:dir3:./:/')
TRACE_OUTPUT = $\langle{\tt integer:1}\rangle$	0	modulus for writing information about optimization iterations: 0 for nothing

Description:

This command specifies the file for the subsequent optimization tracing output. It is useful for separating tracing output for different models constructed in a single run of MODELLER. The tracing output is only produced if TRACE_OUTPUT is larger than 0. The tracing file includes the iteration number, number of function evaluations, function value, average and maximal atomic shifts, the size of the gradient vector, kinetic energy (for molecular dynamics `optimization' only), temperature (MD only) and total energy. This is written out in every TRACE_OUTPUT-th cycle of whatever optimization method is used, starting with the state just before the optimization (iteration 0).

When using the model script for comparative modeling, there is one .D file for each .B file with a model. The .D files contain information about the progress of optimization, from the beginning to the end. The most important column is column 3, which contains the value of the objective function, which is being optimized, as a function of the iteration step (every 10 steps, by default). Thus, the best model, according to MODELLER, is the one that has the lowest number in the third column of the last line of its .D file. This value is also written out in the REMARK record of the PDB file containing the model and in the log file.

Table 2.5:

Column	Description
1	iteration number within one step of the variable target function method
2	number of function evaluations within one step of VTFM
3	objective function value
4	average atomic shift
5	maximal atomic shift
6	proportional to the gradient
7	kinetic energy
8	temperature for molecular dynamics optimization
9	total energy (kinetic and potential; potential = objective function value)

Example: See OPTIMIZE command.