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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
|
| DJSTEST | 0.1 | Tests ABNER
|
| 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
|