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 3.2:
Columns in an optimization trace file.
| 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) |
|
