In previous versions of this manual, several sections included copies of BatchMin test files. Since we provide these test files as part of the standard MacroModel distribution, we have replaced these sections of the manual with a description of the location and contents of the BatchMin test directories.
MMOD_ROOT/run/test subdirectory. The test subdirectories that pertain to BatchMin are as follows. The suite of tests in any directory can be run at your site by editing, then executing, the file called do in that directory.
bmin.app1: This directory contains tests formerly shown in Appendix 1 of the BatchMin Reference Manual and in the section entitled BatchMin Tests. The contents consist of energy evaluations of test molecules using a variety of force fields. Rerunning test evaluations at your site would verify that the program is properly installed and that the test energies found agree with those obtained by us.
bmin.test: This is our standard test suite for program correctness. It tests correctness of energetic procedures (such as minimization) as well as of simple energy evaluations. It is not, however, exhaustive; that is, things can go wrong which are not revealed by the results of this suite. It is normal for small numerical variations to occur between versions of BatchMin compiled on different hosts and even on the same host at different compilation levels. Larger variations can and do build up when long or random trajectories are followed, as in molecular-dynamics and conformational-search procedures. Thus, interpreting the results of these tests requires a certain amount of experience.compare is included in this directory. This runs the diff (or, on SGI, the gdiff) program on two sets of test-suite results, after filtering out certain irrelevant lines. The command syntax is: compare suite1 suite2
suite1 and suite2 are files containing results of the test suite to be compared.
bmin.longtest: This is an extended version of the standard test suite (bmin.test), used to obtain small-molecule timing benchmarks. The procedures do not differ from those in bmin.test, but each procedure is run for a longer period of time (e.g., tighter convergence criteria for minimization, more steps for conformational search, longer times for molecular dynamics). Certain procedures may be better converged in this suite than in the standard suite, leading to less variation from machine to machine or from one to another compiled version.
bmin.simple: The Command Files for Standard Operations given in the MacroModel Primer.
bmin.time: Large-molecule minimizations and dynamics runs, for benchmarking purposes.