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30.10 CONGEN Test Cases

The test cases may be found in CGT (as well as their developmental counterparts). All of these file generate output files which are to be compared with previous runs. In addition, some of the tests will generate other files which have the same file name, and these should be compared too. Scratch files have file names of FOO and file types which begin with the file name. For example, DYNTEST1 generates a number of scratch files named, FOO.DYNTEST1_nn, where nn is the unit number. These files should be deleted when the runs complete. The CPU time listed below is given in minutes for version 2 of CONGEN running on a single CPU of a Silicon Graphics 4D/200 series workstation.

Test cases run on platforms other than the Iris can be found in subdirectories under $CGT whose names match the platforms. For example, the Cray test case outputs are found in $CGT/unicos.

All the tests are run using the equivalent of the RUNCG command. On Unix machines, there are makefiles in both directories for running the test cases, and on VMS machines, there is a descrip.mms file. A target of diffs will make difference files for all the test cases.

The differences are always run through the program, ndiffpost, see Ndiffpost, and the output are written to files which have a suffix of .dif. The raw difference files are output to files which have a suffix of .dif.raw.

File Name CPU Time* (min) Purpose

AM94CYCLE 1.9 Test of AMBER94 using a cyclic peptide. Modified from CGCYCLE.
AM94GENER 0.1 Simple generation test for AMBER94.
AM94SPL 2.6 Test of splicing using AMBER94.
AM94TEST1 4.4 Construction of all major residues in the AMBER94 topology file.
AM94TEST2 3.1 Repeat of first AMBER 3 demonstration run, energy calculation of alpha-lytic protease.
AM94TEST3 0.7 Simple conformational search testing AMBER94 energy calculation.
AM94TEST4 0.4 Test minimized ring constructions for AMBER94.
AM94TEST5 0.1 Checks the backbone and sidechain degrees of freedom work correctly at the endpoints of chains and prolines. Modified from CGTEST9.
AM94TEST6 0.6 Test parser errors when AMBER94 is used. Modified from CGTEST1.
AM94TEST7 2.3 Test D amino acid construction. Modified from CGTEST14.
AM94TEST8 2.2 Test AMBER 94 amino acid constructions. Modified from CGTEST15.
AMTEST1 0.4 Amber test 1, check terminal charges, part 1
AMTEST2 0.3 Check terminal charges, part 2
AMTEST3 0.6 Check conformational search with DNA protein complex.
AMTEST4 0.1 Test multi-term torsion term and conformational search.
AMTEST5 0.1 Test hydrogen bond term.
AMTEST6 0.3 Test amino acid construction in conformational search.
AMTEST7 0.2 Test antibody loop construction using AMBER potential.
BRBTEST 0.1 Tests Builder, Newton-Raphson minimization, and vibrational analysis.
CGCYCLE 6.4 Tests construction of cyclic peptides.
CGFIX 0.2 Test fixed atom construction in CONGEN.
CGFIX2 1.2 Test mixture of fixed atom and regular construction in conformational search.
CGHBUILD 0.2 Tests partial sidechain construction in the context of rebuilding hydrogen bonds.
CGMERGE 0.2 Tests merging of conformation files.
CGPARA1 1.8 Tests parallel processing in searching. The time given is the elapsed time.
CGPBE 17.1 Tests use of Poisson-Boltzmann equation with conformational search.
CGPBE2 21.4 Tests parallel implementation of PBE with conformational search.
CGPBE3 3.7 Test parallel conformational search using serial PBE evaluation.
CGRAND 0.3 Tests random node evaluation.
CGRESTART 2.1 Tests restarting when directed searching is done and MIX strategy used. (Currently fails on the CONVEX in malloc. No real idea why).
CGRESTART2 1.6 Repeat of CGRESTART, but without restart step. Output should match CGRESTART except for command processing.
CGRESTART3 6.9 Tests restarting when depth first search is used.
CGRESTART4 6.8 Repeats CGRESTART3 without restarting. Output should match CGRESTART3 except for command processing.
CGTEST1 0.1 Checks the CGEN parser. Many error messages are tested and no conformation file is written.
CGTEST2 0.2 Check ALL and FIRST sidechain construction options
CGTEST3 0.2 } Together, CGTEST3 and CGTEST4 check that the optimization
CGTEST4 0.7 } of the sidechain search for FIRST and ALL in the case where sidechains interact. CGTEST3 has the optimization, whereas CGTEST4 omits it. The CG files generated by both tests should match each other except for the first record, but CGTEST4 should take more CPU time.
CGTEST5 0.3 } CGTEST5 and CGTEST6 verify that the CLSA optimization
CGTEST6 0.5 } used with backbone degrees of freedom works correctly. The CG files should be the same, but CGTEST6 should take longer to get the results.
CGTEST7 0.6 Checks the energy calculations in the sidechain degree of freedom.
CGTEST8 0.5 Checks esoterica of CLSA and CLSD options
CGTEST9 1.9 Checks backbone termini processing and handling of prolines in both backbone and chain closure.
CGTEST10 0.9 Checks all sidechain construction options
CGTEST11 0.2 Tests van der Waals avoidance and Nosymmetry options in a single sidechain construction.
CGTEST12 2.6 Test of van der Waals avoidance in context of full search. Iterative option.
CGTEST13 0.9 Similar to CGTEST12 except Independent option used.
CGTEST14 6.4 Test of D amino acid construction and all amino acid sidechains
CGTEST15 6.4 Similar to CGTEST14, except we test the all hydrogen topology file.
CGTEST16 1.1 Simple test of overlapping degrees of freedom.
CGTEST17 0.5 Second test of overlapping degrees of freedom (sidechains).
CGTEST18 0.7 Test of coordinate writing and energy display filters.
CGTEST19 1.9 Test of ALLCISTRANS options.
CGTEST20 0.1 Test of other non-bonded energy calculations.
CGTEST21 0.1 Test RDEPTH search option.
CGTEST22 1.5 Test cavity energy calculation.
CGTEST23 1.7 Test combination of cavity and PBE energies.
CGTEST24 0.5 Test Worst RMS evaluation option.
CGTEST25 0.5 Test SGRID SELECT and AUTO options.
CGTEST26 4.2 Test cavity energy in evaluate degree of freedom.
CONGEN 0.3 A simple conformational search over five residues
CONGEN2 0.4 A two part conformational search over five residues
CORMANTST 0.1 Tests some coordinate manipulations.
CORTST1 0.1 A virtually worthless test of the correlation functions
DELTEST 0.1 Tests deletion by value in the analysis section
DRAWTEST 0.1 Tests drawing capability of the program.
DYNTEST1 0.2 A series of tests on the dynamics algorithms. Not a complete test. Checks Gear and Verlet algorithms, SHAKE, ability to fix atoms in place. Also checks that the analysis facility can rotate a trajectory with respect to a fixed coordinate set. Some simple checks of dynamics analysis

are also present.

GAUSSIAN 6.0 Test of interface to Gaussian 92.
GENERTEST 0.1 Tests some of the generation and patching routines.
GEPOL 0.1 Test GEPOL surface calculation.
GEPOL2 4.9 Test incremental GEPOL options.
GEPOL3 4.8 Another incremental GEPOL test.
H2OTST 0.1 Runs a water dimer to convergence and a true minimum. Also tests TLIMIT option.
HBCOMP 0.5 A self comparison of hemoglobin. Tests the comparison command in the analysis facility
HBMBCOMP 1.4 A comparison of hemoglobin to myoglobin. Tests comparison command and construction of difference tables.
ICTEST 0.1 Tests the routine that deal with internal coordinates.
IMH2OTEST 0.4 Water with periodic boundaries
IMPTEST0 0.1 Inducible multipole code, volume test.
IMPTEST1 0.1 Inducible multipole code, dimer test.
IMPTEST2 0.1 Small molecule test, analysis interface.
IMST2TEST 0.5 ST2 water with periodic boundaries.
IMTEST 0.1 Checks Images for a small system with C2 symmetry.
JTEST1 0.2 J coupling calculations on one leucine.
JTEST2 0.2 Ensemble averaging of J coupling calculations on two leucines.
JTEST3 0.2 J coupling calculations on one leucine with J errors.
JTEST4 0.3 Ensemble averaging of J coupling calculations on two leucines with joining with convergence tests.
JTEST5 0.1 Four leucine J coupling, ensemble averaging test with real data.
NANATST1 0.8 Tests most of the features of the analysis facility
NANATST2 0.7 Tests more features of the analysis facility
NANATST3 1.5 Tests the dynamic properties in the analysis facility
NOETEST 0.2 Tests NOE constraint calculations and calculation of energy derivatives.
NOETEST2 0.1 Test NOE ensemble averaging on a three atom system
NOETEST3 0.1 Test NOE ensemble averaging on a four atom system
NOETEST4 0.5 Test NOE code on a larger system.
NOETEST5 0.1 Test NOE code on beta hairpin using real data.
PBETEST 9.1 Test Poisson-Boltzmann electrostatics.
PBETEST2 1.5 More PBE testing. Thorough testing of options.
PBETEST3 0.1 Test of dielectric smoothing.
PBETEST4 0.1 Test of dielectric cavity
PBETEST5 0.3 Test of cavity in a Debye-Huckel fluid.
PBETEST6 4.2 Test of molecular surface usage in PBE code.
PBETEST7 5.5 Test of charge anti-aliasing
PBETEST8 1.1 Test of dielectric smoothing in a protein.
PBETEST9 0.1 Test of dielectric combination rules
PBETEST10 1.6 Test of dielectric constant modification based on accessible surface.
PBETEST11 0.2 Test of margin option.
PBETEST12 3.9 Margin and origin test using BPTI
PDBTEST1 0.4 Test #1 of Brookhaven Data Bank reading. Read tendamistat.
PDBTEST2 0.7 Test #2 of Brookhaven Data Bank reading. Read Fab KOL.
READTEST 0.1 Incomplete test of coordinate reading.
READTEST2 0.1 Test of sequence reading by atom.
READTEST3 0.1 IDREAD reading in PDB.
READTEST4 0.1 Test of alternate coordinate reading in PDB I/O.
READTEST5 0.1 Test of alternate model reading in PDB I/O.
SEARCHNOE 0.3 Tests conformational search with NOE's and also runs some simple tests of All Hydrogen construction.
SPHERE 2.7 Rudimentary test of sphere drawing.
ST2TEST 0.2 ST2 water without boundary conditions.
SURFTST 0.2 Checks the accessible surface calculation
TEST 0.1 Short test that hits a lot of stuff. Must always be run.
TESTCONS 0.7 Tests the harmonic constraints.
TESTCONS2 1.9 Tests the interaction of dihedral and J coupling constraints with the conformational search.
TESTHB 0.1 Test hydrogen bond calculations.
TESTHOM 1.7 Test homology finding code.
TESTPARM 0.1 Test AMBER parameter reading code.
TESTRTF 0.4 Tests the RTF I/O commands, and a simple test of PEER output
TESTRTF2 0.1 Test of charge generation in the RTF code.
TESTRTF3 0.1 Test automatic generation code on three and four membered rings.
TESTSEL 0.4 Tests the atom selection routines and use of wildcards in commands in the analysis section
TESTSPL 0.2 Tests SPLICE command
TRANSFORM 1.4 Tests coordinate transformation commands.
TWIST 0.1 Tests TWIST command in the analysis facility
VIBRTST 0.1 Tests vibrational analysis
* The CPU time is for code not optimized by the compiler.