CHARMM Testcases
The CHARMM test cases are designed to test features of CHARMM and some of
error handling. Though the test cases are not designed as a tutorial and
some used options and input parameters are not recommended, the test cases
are a valuable learning tool in setting up input files for CHARMM.
* Menu:
* Overview:: Notes about testcases
* Instruction:: How to run testcases
* C20TEST:: Description of testcases in c20test
* C22TEST:: Description of testcases in c22test
* C23TEST:: Description of testcases in c23test
* C24TEST:: Description of testcases in c24test
* C25TEST:: Description of testcases in c25test
* C26TEST:: Description of testcases in c26test
* NBONDTEST:: Description of testcases in cnbondtest
* MMFFTEST:: Description of testcases in cmmfftest
* GRAFTEST:: GRAPHICS Testcases
Notes about the Testcase Suite
Testcases are reformed. All testcases before version 22 are collected
in ~/cnnXm/test/c20test and new tests are written while we develop
CHARMM. The new testcases are gathered in ~cnnXm/test/c22test,
c23test, ... Note the following.
(1) In the new testcase suite, we use formatted I/O for
topology/parameter files in order for all testcases to run
independently each other.
(2) We make testcases self-contained whenever possible. If external
data files are required to run the test, they are in ~/cnnXm/test/data.
(3) CHARMM command parameter 0 and 9 are reserved to point
directories for data and scratch files. These are defined in
the stream file ~/cnnXm/test/datadir.def. The default
definitions are
set 0 data/
set 9 scratch/
(4) We do not include benchmark suite in the distribution package
any more. Benchmarks produced on some Harvard local machines are
available upon request.
(5) A developer must run all the testcases and confirm the benchmarks
before he send in his developmental version. If he develops a
new function, he has to provide proper testcases.
How to Run Testcases
In order to run testcases, you have to locate ~/cnnXm/test/datadir.def
and review the content. It directs the directories for data and
scratch files needed for testcases. Since the stream file is
stream'ed at the beginning, you may specify other job characteristics
in the file, e.g., bomb level (by the BOMLEV command), FASTer level, etc.
A C-shell script is provided in ~/cnnXm/test/test.com, which expects
at least one argument.
test.com host_machine_type [ output_dir benchmark_dir target_executable ]
(1) host_machine_type can be convex, cray, ibmrs, sgi, stardent, sun, etc.
and must be specified.
(2) output_dir is an optional argument which indicates the directory
where you collect output files. The default is output.
(3) benchmark_dir is an optional and points the directory that
contains benchmark files. If you specify 0 for this argument,
then no comparison is done.
(4) target_executable is the executable you are testing. If not specified
the default executable, ~/cnnXm/exec/{host_machine_type}/charmm, is
used.
For example, if your host is a Convex and you want run under the
default setting, your command is
test.com convex
When test.com is finished, you may find the report file that
records differences between the test output and the target benchmark.
Normally the report file is named as {output_dir}.rpt. The review
may indicate small numeric discrepancies due to different machine
precision and compiler options used.
For non-vector machines such as SGI, SUN, etc., ignore the warning
message "***** No VECTOR code compiled."
Testcases from CHARMM20
~charmm/test/c20test contains 48 testcases inherited from CHARMM20
test set (the VAX version CHARMM20 and previous). All external file
I/O are done in CARD format and binary I/O testing is performed by
stdtest in c22test.
(1) brbtest.inp
File : toph8.rtf/param3.prm
Model: AMN-CBX-AMN-CBX
Test : (1) IC PARAM, IC EDIT, IC SEED, IC BUILD
(2) COOR COPY, COOR ORIENT MASS
(3) HBOND
(4) MINI CONJ NSTEP 100
(5) MINI NRAPH NSTEP 40
NOTE : I/O in card format
BRBTEST.CRD inserted.
(2) constest.inp
File : toph9.rtf/param6.prm
Model: TRP
Test : Various CONStraint commands
NOTE : BOMBLEV set to -2 to read param6.inp
Modified to test proper dihedral constraints by Arnaud Blondel
(15-Feb-94)
(3) control.inp
File : None
Model: None
Test : CMDPAR and flow control
(4) djstest.inp
File : toph10.rtf/param7.prm, bpti.crd
Model: PTI (58aa) and 4 waters
Test : ABNER minimization and various electrostatic options
Note : Was reduced to hepta peptide with one water model.
Recover the original model since it talks 1.44 CPU min.
on Convex C220. The coordinates are read from bpti.crd.
djstest.crd is no longer required.
(5) dyntest1.inp
File : toph8.rtf/param3.prm
Model: TRP
Test : DYNAmics commands with various CONStraints
(6) dyntest2.inp
File : toph8.rtf/param3.prm
Model: TRP
Test : DYNAmics LANGevin commands with various CONStraints
(6a)dyntest3.inp (from R. Stote)
File : toph8.rtf/param3.prm
Model: TRP
Test : TESTS A NUMBER OF DYNAMICS RESTART CALCULATIONS
(7) enbtest.inp
File : None
Model: CO-NH
Test : Various nonbonded interaction options using VIBRAN commands
on selected energy terms
(a) Hydrogen bond energy, (b) van der Waals energy
(c) Atom electrostatics, (d) Group electrostatics
(e) Extended electrostatics
Note : FASTer OFF in order to use SKIPE commands
(8) enertest.inp
File : toph10.rtf/param8.prm, bpti.crd
Model: PTI and 4 waters
Test : ENERGY/GETE commands for selected energy terms (SKIPE)
under various FAST/nonbond options.
Forces are also examined.
(9) genertest.inp
File : toph8.rtf/param3.prm
Model: GLY-PRO, PRO-GLY, PRO-PRO
Test : some of the generation and patching routines
(10) h2otst.inp
File : toph8.rtf/param3.prm
Model: two waters
Test : HBONd and NBONd commands then MINI ABNR/NRAPH
Runs a water dimer to convergence and a true minimum.
(11) hbondtest.inp
File : toph9.rtf/param6.prm
Model: RNase beta sheet part 1 (PRO VAL ASN THR PHE VAL HSC)
RNase beta sheet part 2 (SER ILE THR ASP CYS ARG GLU)
and 5 waters
Test : HBUIld and HBOND commands
Note : ANAL command testing commented out
(12) hbuildst2.inp
File : toph9.rtf/param6.prm
Model: RNase beta sheet part 1 (PRO VAL ASN THR PHE VAL HSC)
RNase beta sheet part 2 (SER ILE THR ASP CYS ARG GLU)
and 5 ST2 waters
Test : HBUIld and HBOND commands
(13) ictest.inp
File : toph8.rtf/param4.prm
Model: AMN-CBX
Test : internal coordinate and coordinate manipulation commands
(14) imbetash.inp
File : toph9.rtf/param6.prm
Model: ALA-ALA betasheet
Test : build a beta sheet by IMAGe/IMPAtch commands
ABNR 25 step minimization
(15) imh2otest.inp
File : toph8.rtf/param3.prm, cubic.img, wat125.crd
Model: Box of 125 OH2 waters
Test : 10 step dynamics in cubic periodic boundary condition
Note : imh2otest.img renamed to cubic.img
imh2otest.crd renamed to wat125.crd
(16) imst2test.inp
File : toph9.rtf/param6.prm
Model: Box of 125 ST2 waters
Test : 10 step dynamics in cubic periodic boundary condition
Note : imst2test.img renamed to cubic.img
imst2test.crd renamed to st2125.crd
dynamics performed.
(17) imtest.inp
File : toph9.rtf/param6.prm
Model: ALA 9-mer betasheet
Test : Build C2 rotated image and 100 step ABNR minimization
Note : imtest.img and imtest.crd are inserted
(18) langtest1.inp
File : None
Model: 4 extended atom butane
Test : 2500 step Langevin dynamics with FBETA 6.657235
(19) langtest2.inp
File : None
Model: 4 extended atom butane
Test : 100000 step Langevin dynamics with FBETA 100.0
(20) lsqptest.inp
File : toprna10r.rtf/pardna10.prm
Model: GUA-CYT
Test : COOR LSQP (least-squares-plane) commands
(21) maatest.inp
File : None
Model: N-methyl alanyl acetamide
Test : Dihedral constraint ABNR minimization to mimic Uray-Bradley
terms. Then, release the constraint and further ABNR-NRAPH
minimize. Perform VIBRAN.
Note : maatest.crd inserted.
(22) nbondtest.inp
File : toph19.rtf/param19.prm, bpti.crd
Model: PTI and 4 waters
Test : FASTer ON/OFF nonbond interaction energy
(23) noetest.inp
File : toph19.rtf/param19.prm, bpti.crd
Model: PTI and 4 waters
Test : NOE distance restraints
Note : bpti.crd is used instead of noetest.crd (identical)
(24) partest.inp
File : toprna10r.rtf/pardna10.prm, partest.prm
Model: GUA-CYT dimer
Test : parameter file I/O
Note : partest.par renamed to partest.prm
(25) patchtest.inp
File : toph9.rtf/param6.prm
Model: seven HSC residue segment
Test : patch
(26) powelltes.inp
File : toph9.rtf/param6.prm, bpti.crd
Model: PTI and 4 waters
Test : MINI POWEll with SHAKE and HARMonic constraints
Note : powelltes.man and powelltes.sol are replaced by bpti.crd
TIP3 waters are used instead of ST2 waters.
(ST2 minimization is found in rigidst2.inp)
(27) psftest.inp
File : toph9.rtf/param5.prm, rtftest.psf
Model: PRO-PRO-PRO and ALA-ALA-ALA
Test : PSF I/O
(28) quasi.inp
File : toph9.rtf/param5.prm
Model: Ethanol
Test : VIBRAN, quasiharmonic dynamics
(29) rgyrtest.inp
File : toprna10r.rtf/pardna10.prm
Model: ADE-CYT-GUA-URI
Test : COOR RGYR
(30) rigidst2.inp
File : toph9.rtf/param6.prm
Model: two ST2 waters
Test : HBUILD, TEST FIRST, Constraint/unconstraint minimization
and dynamics
(31) rtftest.inp
File : param5.prm, rtftest.rtf, toprna10r.rtf
Model: 21 amino acid sequence
Test : RTF I/O
(31a) rtf2.inp [Ryszard Czerminski, 30-Apr-92]
File : all *rtf files from data directory
Test : removing old residues when reading rtf append
Note : does not work properly (yet)
(32) sbdtest1.inp
File : toph10.rtf/param7.prm, sbdtest1.pot
Model: TIP3 water
Test : SBOUNDARY and energy due to the boundary potential
(33) sbdtest2.inp
File : toph10.rtf/param7.prm, sbdtest2.pot
Model: ST2 water
Test : SBOUNDARY and energy due to the boundary potential
(34) sbpgentst.inp
File : sbpgentst.sbt
Model: None
Test : SBOUNDARY POTENTIAL
(35) simp.inp
File : toph9.rtf/param5.prm
Model: AMN-CBX, AMN-CBX
Test : COOR ORIENT, Q commands
Note : simp.crd is inserted
(36) st2test.inp
File : toph9.rtf/param6.prm, st2125.crd
Model: 125 ST2 waters
Test : 15 step Verlet dynamics
Note : st2test.crd renamed to st2125.crd
(37) surftst.inp
File : toph9.rtf/param6.prm, bpti.crd
Model: PTI and 4 waters
Test : COOR SURFace and COOR CONTact commands
Checks the accessible surface calculation.
Note : use full BPTI structure instead of a shortened one.
surftst.chr is no longer needed.
(38) test.inp
File : toph8.rtf/param4.prm, bpti.crd
Model: PTI and 4 waters
Test : HBUILD, 10 step Verlet dynamics, INTERaction, MINI CONJ
Note : use full BPTI structure instead of a shortened one.
test.crd is no longer needed.
(39) testcons.inp
File : top9.rtf/param6.prm, lysozyme.crd
Model: Lysozyme (129aa)
Test : Harmonic atom constraints
Note : testcons.src renamed to lysozyme.crd
(40) testsel2.inp
File : toph8.rtf/param4.prm
Model: part of PTI sequence (60 atoms)
Test : atom and tag selection, define command
Note : test.crd is inserted
(41) tipstest.inp
File : tip125.crd, cubic.img
Model: box of 125 TIP3 waters
Test : energy with and without minimum image convention
Note : topwat.inp and parwat.inp inserted
tipstest1.crd replaced by tip125.crd
tipstest1.img replaced by cubic.img
tipstest1.inp renamed to tipstest.inp
(42) trnphi.inp
File : toph8.rtf/param3.prm
Model: TRP
Test : 500 step dynamics, MONITOR, MERGE, CORREL commands
Note : trnphi.crd is inserted
(43) vibpafl.inp
File : None
Model: All hydrogen methane
Test : VIBRAN DIAG, READ, EDIT and PAFL commands
(44) vibran.inp
File : toph9.rtf/param6.prm
Model: TRP
Test : VIBRAN commands
(45) vibrtst.inp
File : toph8.rtf/param3.prm
Model: AMN-CBX, AMN-CBX
Test : VIBRAN commands
Note : vibrtst.crd inserted
(46) vibwat.inp
File : None
Model: a water
Test : VIBRAN commands
(47) voltest.inp
File : toph10.rtf/param8.prm, bpti.crd
Model: BPTI
Test : SCALAR and COOR VOLUME commands
Note : voltest.crd is replaced by bpti.crd
(48) xray.inp
File : toph10.rtf/param8.prm, bpti.crd
Model: BPTI
Test : WRITE XRAY command
Note : enertest.crd is replaced by bpti.crd
New Testcases in CHARMM Version 22
The following tests are written during the CHARMM22 development
period. Note that most tests are self-contained and only lengthy
data files are left out in the data directory. We also need to use
toph19.rtf/param19.prm. stdtest test most CHARMM commands supported
in the version.
[1] General Tests
(0) stdtest.inp [Ryszard Czerminski, 20-Dec-91]
File : toph19.rtf/param19.prm
Model: ALA-TRP
Test : most CHARMM commands
(1) block1.inp [Bruce Tidor]
File : topnah1r.rtf/parnah1r.prm, gal11.crd
Model: GAL11 (dimer of ADE-ADE-GUA-THY-GUA-THY-GUA-ADE-CYT-ADE-THY)
Test : patch and block commands
Note : used to be self-contained. RTF, PARAM and CRD are separated
out to topnah1r.rtf, parnah1r.prm and gal11.crd respectively.
(2) block2.inp [Ryszard Czerminski, 11-Dec-91]
File : None
Model: Methanol (Me-OH to HO-Me mutation)
Test : BLOCK FREE energy calculation
Note : command line parameters 1-8 in use
(3) cortst.inp
File : None
Model: ACE GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY CBX
Test : 100 step dynamics and CORRelation commands
Note : modified from the VAX version cortst.inp.
self-contained. NOT working on some machines.
(4) covaritst.inp [Charlie L. Brooks III, 09-Dec-91]
File : None
Model: deca-alanine
Test : 50 step dynamics and cross correlation calculation
COOR COVAriance command
(5) ewions.inp [Roland Stote and Stephen Fleischman, 04-Dec-91]
File : None
Model: 108 Na(+)Cl(-) in a cubic box
Test : Ewald summation energy under various FAST options.
(6) exsgtst.inp [Ryszard Czerminski, 11-Dec-91] ! TO BE REMOVED !!!
File : toph19.rtf/param19.prm, bpti.crd
Model: BPRI
Test : UPDATE/ENERGY EXSG subcommand
(6a)exsg.inp [Ryszard Czerminski, 26-Mar-92]
File : None
Model: four hydrogen atoms
Test : UPDATE/ENERGY EXSG subcommand
(7) fshake1.inp [Stephen Fleischman, 04-Dec-91]
File : cubic.img, tip125.crd
Model: Glycerol in 125 water periodic box
Test : SHAKE FAST against normal SHAKE
(8) fshake2.inp [Stephen Fleischman, 04-Dec-91]
File : cubic.img, tip125.crd
Model: 125 water periodic box
Test : SHAKE FAST against normal SHAKE
(9) icfix.inp [Charlie L. Brooks III, 09-Dec-91]
File : None
Model: Three methane molecules
Test : TSM ic constraint commands
(10) icpert.inp [Charlie L. Brooks III, 09-Dec-91]
File : tip125.crd, cubic.img
Model: ACE-ALA-CBX in 125 TIP3 water periodic boundary box
Test : the internal coordinate constraint and TSM commands
(11) mewtest.inp [Charlie L. Brooks III, 09-Dec-91]
File : mewtest.crd, cubic.img
Model: Methane in 245 TIP3 water rectangular periodic boundary box
Test : non-linear lambda scaling for methane -> nothing perturbation
(12) slowgr.inp [Charlie L. Brooks III, 09-Dec-91]
File : None
Model: Ethanol -> Propane
Test : TSM slow growth free energy simulation example
(13) solanal.inp [Charlie L. Brooks III, 09-Dec-91]
File : tip216.crd, cubic.img
Model: 216 water molecules in a periodic box
Test : solvent analysis on water
(14) window.inp [Charlie L. Brooks III, 09-Dec-91]
File : None
Model: Ethanol -> Propane
Test : TSM window/TI free energy simulation example
(15) path.inp [Ryszard Czerminski, 11-Dec-91]
File : None
Model: Alanine Dipeptide
Test : PATH between minima
Note : NOT working, YW 17-Dec-91
(16) pert.inp [Ryszard Czerminski, 11-Dec-91]
File : None
Model: Methanol (Me-OH to HO-Me mutation)
Test : Free energy perturbation calculation by PERT command
(17) travel.inp [Stefan Fischer, 20-Jun-91]
File : chair.crd, boat.crd
Model: Cyclohexane
Test : TRAVEL commands
(18) umbrella.inp [Jeyapandian Kottalam & Youngdo Won, 10-Dec-91]
File : None
Model: Cyclohexane
Test : RXNCOR commands
(19) xtlala1.inp [Martin J. Field, 22-Nov-90]
File : None
Model: Alanine crystal
Test : COOR CONVERT and CRYSTAL commands. Crystal optimization.
Note : xtl_ala[1-4].inp are merged into this testcase
(20) xtlala2.inp [Martin J. Field, 22-Nov-90]
File : None
Model: Alanine P1 crystal
Test : CRYSTAL commands. Crystal vibration and phonon analysis.
Note : xtl_ala[5-6].inp are merged into this testcase
(21) xtlala3.inp [Martin J. Field, 24-Jan-91]
File : None
Model: Alanine P1 crystal
Test : two 100 step CPT dynamics
Note : xtl_ala7.inp renamed to xtlala3.inp
[2] Energy Tests
(1) cuttest1.inp [Stephen Fleischman, 04-Dec-91]
File : toph19.rtf/param19.prm, bpti.crd
Model: BPTI with four crystal waters
Test : energy and force under various ATOM electrostatic cutoff
options and VATOM VSWITCH with truncated cutoff (i.e.,
CTONNB = CTOFNB).
(2) cuttest2.inp [Stephen Fleischman, 04-Dec-91]
File : toph19.rtf/param19.prm, bpti.crd
Model: BPTI with four crystal waters
Test : energy and force under various ATOM electrostatic cutoff
options and VATOM VSHIFT.
(3) cuttest3.inp [Stephen Fleischman, 04-Dec-91]
File : toph19.rtf/param19.prm, bpti.crd
Model: BPTI with four crystal waters
Test : energy and force under various ATOM electrostatic cutoff
options with van der Waals interactions skipped.
(4) cuttest4.inp [Stephen Fleischman, 04-Dec-91]
File : toph19.rtf/param19.prm, bpti.crd
Model: BPTI with four crystal waters
Test : energy and force under various ATOM electrostatic cutoff
options and VATOM VSWITCH.
(5) cuttest5.inp [Stephen Fleischman, 04-Dec-91]
File : toph19.rtf/param19.prm, bpti.crd
Model: BPTI with four crystal waters
Test : energy and force under various VATOM van der Waals options
with electrostatic interactions skipped.
(6) ew14test.inp [Stephen Fleischman, 04-Dec-91]
File : tip125.crd, cubic.img, ew14test.str
Model: Glycerol in 125 TIP3 water periodic box
Test : Ewald energy calculation with exclusions
(7) ewh2oderiv.inp [Stephen Fleischman, 04-Dec-91]
File : tip125.crd, cubic.img, ewh2oderiv.str
Model: 125 TIP3 water periodic box
Test : Ewald derivative and energy with various van der Waals
cutoff options
(8) ewh2oexcl.inp [Stephen Fleischman, 04-Dec-91]
File : tip125.crd, cubic.img
Model: 125 TIP3 water periodic box
Test : Ewald nonbond exclusions
[3] Dynamics Test
(1) ewtipdyn.inp [Stephen Fleischman, 04-Dec-91]
File : tip125.crd, cubic.img
Model: 125 TIP3 water periodic box
Test : DYNA VERLET 50 step with EWALD and SHAKE (FAST)
FASTer VECTOR, SCALAR and OFF with either VSWITCH or VSHIFT
[4] QUANTUM
(1) quantum1.inp [Jeff Evansec, 28-May-92]
File : none
Model: monohydrated acetone
Test : quantum mechanics / molecular mechanics
New Testcases in CHARMM Version 23
The following tests are written during the CHARMM23 development period.
New features and major modifications are tested with the testcases.
(1) clustst.inp [Mary E. Karpen, 09-Jan-93]
File : clustst.hex
Model: YPGDV peptide
Test : CLUSter
(2) cmdpar.inp [Leo Caves, 18-Jan-1994]
File : None
Model: None
Test : command line parameters: assignment,substitution and manipulation.
Note : error handling tested. one temporary file created to test import
of parameter from external file.
(3) mmfptest.inp [Benoit Roux, 31-Jan-94]
File : toph19.inp, param19.inp
Model: tripeptide ASP-ALA-ARG
Test : miscelaneous boundary and restraints
Note : command line parameters 1 in use
(4) mtsm1.inp [Masa Watanabe, 18-Aug-1993]
File : toph19.rtf and param19.prm
Model: Met-enkephalin
Test : Multiple time-step Method (MTS)
(5) mtsm2.inp [Masa Watanabe, 18-Aug-1993]
File : toph19.rtf and param19.prm
Model: Met-enkephalin
Test : MTS method with Nose-Hoover heat bath
(6) nmrtest1.inp [Benoit Roux, 31-Jan-94]
File : toph19.inp, param19.inp
Model: tripeptide ASP-ALA-ARG
Test : generate trajectory and calculate NMR properties
Note : command line parameters 1 in use
(7) nose1.inp [Masa Watanabe, 18-Aug-1993]
File : toph8.rtf and param3.prm
Model: TIP3P water in a box
Test : Single Nose-Hoover Dynamic Method
(8) nose2.inp [Masa Watanabe, 18-Aug-1993]
File : None
Model: A ethane molecule in TIP3P water
Test : Nose-Hoover Method with multiple heat bath
(9) replica.inp [Leo Caves, 18-Aug-1993]
File : toph19.inp, param19.inp
Model: alanine dipeptide
Test : replication of PSF; energy,forces and nonbonded exclusions.
Note : nonbonded exclusions cannot be tested for all list generation
routines on a given machine (eg. CONVEX specific FNBL).
(10) rism.inp [Georgios Archontis, 18-Aug-1993]
File : None
Model: pure solvent: tip3p water
solute 1: extended-carbon with weak charge
solute 2: diatomic
Test: solvent-solvent calculation
solute-solvent calculation
solute-solute calculation
calculation of chemical potential of solvation for
the two solutes and decomposition to
energy and entropy of solvation
(11) zmat.inp [Benoit Roux, 31-Jan-94]
File : toph19.inp, param19.inp
Model: TIP3P water dimer
Test : construct the optimized configuration for water dimer
Note : difficult to do with the IC table
New Testcases in CHARMM Version 24
The following tests are written during the CHARMM24 development period.
New features and major modifications are tested with the testcases.
(1) autogen.inp [Rick Venable, 04-Aug-1995]
File : none
Model: alanine tetrapeptide
Test : automatic regeneration of angles and dihedrals
designed for use after multiple PATCh statements
compare PSF before and after; should be identical
Note : patches may now be written w/o ANGL and DIHE terms
the PSF should not contain any water molecules
(2) bcdtest.inp [Wonpil Im, 02-Aug-95]
File : None
Model: Beta-cyclodextrin with 8 crystal waters
Test : Crystal build
Note : introduced to check the unit cell rotation bugfix
(3) block3.inp [Stefan Boresch, 01-Aug-95]
File : datadir.def; data/tip125.crd; data/cubic.img;
scratch files (trajectories+restart files) produced.
Model: ethane/methanol hybrid in small TIP3 water box
Test : Tests BLOCK in combination with IMAGE module
Note : Runs a few steps of dynamics and tests the supported
post-processing options
(4) calc.inp [Benoit Roux, 15-Feb-94]
(5) dihtest1.inp [Arnaud Blondel, 15-Feb-94]
File : top_all22_na.inp / par_all22_na.inp
Model: ADE : CYT
Test : Various dihedral energy routines.
NOTE : Introduced to check the correspondance between old
and new dihedral energy routines.
Designed to test various parts of the code.
(6) dihtest2.inp [Arnaud Blondel, 15-Feb-94]
File : None
Model: Extended atom butane
Test : None planar equilibrium dihedral energy terms.
TEST SECOnd command (second derivatives).
NOTE : New dihedral energy routine only.
(7) dimb1.inp [Herman van Vlijmen, 15-Feb-95]
File : None
Model: Deca-alanine
Test : DIMB and DIMB DWIN normal mode calculations
(8) dimb2.inp [Herman van Vlijmen, 15-Feb-95]
File : None
Model: Deca-alanine
Test : Reduced basis diagonalization with compressed Hessian
(9) dyn4Dtest.inp [Carol B. Post, 15-Feb-95]
(10) mmfptest2.inp [Benoit Roux, 15-Feb-94]
(11) mmfptest3.inp [Benoit Roux, 15-Feb-94]
(12) nptdyn.inp [Scott Feller, 01-Aug-1995]
File : tip125.crd
Model: cubic water box
Test : extended pressure system; CPT dynamics
isotropic system with Langevin piston
Note : minimal test, 40 steps
(13) pbound1.inp [Charles L. Brooks, III and William A. Shirley, 15-Aug-95]
File : toph19.rtf, param19.prm, cubic.img, tip125.crd
Model: 125 TIP3P water molecules
Test : The explicit (simple) periodic boundaries (BOUND command)
Note : This test case checks the energy and dynamics of a simple
implementation of explicit periodic boundaries against the
IMAGE facility values. As of c24b1, works only with the
FAST Scalar routine.
(14) pert2.inp [Stefan Boresch, 01-Aug-95]
File : none; on none Unix platforms /dev/null may have to be
changed appropriately.
Model: one bond-length of triatomic symmetric molecule is
changed from 1 to 2 A (gas phase). Various protocols
are used
Test : Tests PERT in combination with SHAKE; constraint correction
Note : The free energy differences for this system can be
calculated analytically; these results are listed at
the end of the input file together with the results
I obtained on one of our HP's. The differences between
simulation and analytical result should give some feeling
as to what to expect on other platforms.
(15) tntest1.inp [P. Derreumaux 28-Jan-94]
File : None
Model: Alanine dipeptide
Test : Truncated Newton Minimizer TNPACK
New Testcases in CHARMM Version 25
The following tests are written during the CHARMM25 development period.
New features and major modifications are tested with the testcases.
(1) allxtl.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : Crystal symmetry test case. Test ALL of the crystal types.
(2) anal.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : long/short energy print-out with the anal command
(3) cortst25.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Model: alfa decaglycine
(4) cwat.inp [Paul Lyne, 01-Sep-1995]
File : libfil.dat, modpot.dat and cwat.str
Model: two water molecules
Test : QM(CADPAC)/MM(CHARMM)
First water is calculated with TIP3P and the second water is
QM-STO3G.
Note : The Hamiltonian and other CADPAC control commands are found in
cwat.str
(5) ewald_atom.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
(6) ewald_grp.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
(7) ewald_pert.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
(8) fastest.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : fast options with various non-bond schemes
Model: BPTI coordinates with all but 4 water removed
(9) gmstst.inp [Milan Hodoscek]
File : none
Model: Alalnine
Test : QM(GAMESS)/MM(CHARMM)
CTERM is QM and the rest is MM. Link atom is between CA and C
Note : Runs ~ 3 min on HP-735
(10) hba1.inp [Lennart Nilsson]
File : top_all22_prot.inp and par_all22_prot.inp
Model: three water molecules
Test : hydrogen bond analysis facility
(11) helix.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : helix analysis code
makes a duplicate of the perfect octamer of CA atoms and
performs coordinates transformations to align it as a helix
in a parallel fashion.
(12) hrbestfit.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : Harmonic restraints best-fit test case
Model: acetamide
Files: toph19.rtf, param19.prm
(13) mtsm3.inp [Masa Watanabe, 09-Feb-1996]
Model: Met-enkephalin
Test : multiple time scaled method
(14) pull.inp [Lennart Nilsson]
Test : application of external forces to the system
(15) quiet.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : a number of dynamics calculations
(16) resdtest.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : restrained distances
(17) rpath1.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : Replica Path method
(18) td149.inp [Bernard R. Brooks, 15-JUL-97 c25b1]
Model: truncated dodecahedron box of 149 water molecules
(19) vibwat25.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : water normal modes
(20) xtloct1.inp
Model: octane crystal
Test : cryst building code using X-cryst fractional coordinates
as starting structure
Ref. : H. Mathisen and N. Norman, Acta Chemica Scandinavica (1961) 15, 1747
New Testcases in CHARMM Version 26
The following tests are written during the CHARMM26 development period.
New features and major modifications are tested with the testcases.
(1) block4.inp [Thomas Simonson, 24-JUL-97, c26a1]
Test : BLOCK enhancement that allows different coefficients for different
energy terms in free energy simulations
Model: hybrid Asn-Asp in vacuum
(2) cftigas.inp [Krzysztof Kuczera, 22-Mar-1997, c26a1]
Test : one-dimensional conformational thermodynamic integration
Model: butane in vacuum
Files: top_all22_prot.inp and par_all22_prot.inp
(3) cftmgas.inp [Krzysztof Kuczera, 22-Mar-1997, c26a1]
Test : CFTM protocol:
(a) Perform MD with holonomic constraints, save gradient file
(b) Perform elementary analysis
Model: ALA10 with all phi and psi constrained, vacuum
Files: top_all22_prot.inp and par_all22_prot.inp
(4) conmin.inp [Krzysztof Kuczera, 22-Mar-1997, c26a1]
Test : energy optimization with holonomic constraints
Model: ALA10 with all phi and psi fixed
Files: top_all22_prot.inp and par_all22_prot.inp
(5) luptst.inp [Krzysztof Kuczera, 22-Mar-1997, c26a1]
Test : Generate butane and run LUP protocol to create path between
trans and gauche minima
Files: top_all22_prot.inp and par_all22_prot.inp
(6) mbtest18.inp [Robert Nagle, 10-JUL-97, c26a1]
Test : MBOND/CHARMM TEST #18
Test MBOND dynamics body-based production runs with different
conditions and different substructuring.
Begins from an body based equilibration.
(7) mbtest19.inp [Robert Nagle, 10-JUL-97, c26a1]
Test : MBOND/CHARMM TEST #19
Test MBOND dynamics body-based production runs with thermostat on.
(8) mbtest24.inp [Robert Nagle, 10-JUL-97, c26a1]
Test : MBOND/CHARMM TEST #24
mode generation/storing
(9) mbtest25.inp [Robert Nagle, 10-JUL-97, c26a1]
Test : MBOND/CHARMM TEST #25 MTS
(10) pathint.inp [Benoit Roux, 10-JUL-97, c26a1]
Test : Classical trajectories for acetylacetone close to
the transition state
Files: top_all22_prot.inp and par_all22_prot.inp
(11) pbeqtest1.inp [Benoit Roux, 10-JUL-97, c26a1]
Test : (1) the Poisson Boltzmann Equation solver for alanine dipeptide
(2) the Atomic Born Radii
(3) the Solvation Forces
Files: top_all22_prot.inp, par_all22_prot.inp and radius.str
(12) pbeqtest2.inp [Benoit Roux, 10-JUL-97, c26a1]
Test : (1) the Poisson Boltzmann Equation solver with membrane
(2) the Solvation Forces with membrane
Files: top_all22_prot.inp, par_all22_prot.inp and radius.str
(13) pm6test1.inp [Benoit Roux]
(14) whamtest.inp [Benoit Roux]
Test : Perturbation calculation with WHAM post-processing
NonBOND Testcases in CHARMM Version 25
The following tests are written during the CHARMM25 development period.
New features and major modifications of nonbonding energy routines are tested
with these testcases.
(1) coul_test.inp [Bernard R. Brooks, 15-JUL-97, c25b1]
Test : calculate coulomb interaction of 2 protons
(2) form.inp [Bernard R. Brooks, 14-Jul-1997, c25b1]
Test : calculate group-group energy (nonbonded) of 2 formamides
(3) form_ewald.inp [Bernard R. Brooks, 14-Jul-1997]
(4) form_ewald_m.inp [Bernard R. Brooks, 14-Jul-1997]
(5) form_fsw.inp [Bernard R. Brooks, 14-Jul-1997]
(6) form_mm_m.inp [Bernard R. Brooks, 14-Jul-1997]
(7) form_simp_m.inp [Bernard R. Brooks, 14-Jul-1997]
(8) ion_fsw.inp [Bernard R. Brooks, 14-Jul-1997]
(9) vdw_test.inp [Bernard R. Brooks, 14-Jul-1997]
MMFF Testcases in CHARMM Version 25
The following tests CHARMM/MMFF features. Common external files are
in the test/data directory:
mmffang.par
mmffbond.par
mmffchg.par
mmffdef.par
mmffoop.par
mmffstbn.par
mmffsup.par
mmffsymb.par
mmfftor.par
mmffvdw.par
mmff_setup.str
(1) mmff.inp [Ryszard Czerminski, 11-May-1993]
Test : MMFF parameter reader, energy & derivatives
(2) mmff_amino.inp [Ryszard Czerminski, 11-May-1993]
Test : new MMFF ring perception code
(3) mmff_append.inp [Ryszard Czerminski, 11-May-1993]
Test : 'read merck ... append' command
(4) mmff_c60.inp [Tom Halgren, 11-May-1993]
Test : PARAMETERS of C60 releated molecular moieties
(5) mmff_clpert.inp [Ryszard Czerminski, 11-May-1993]
Model: chloromethane
Test : PERT command (slow growth method) to calculate free energy
perturbation for migrating -Cl atom in chloromethane
(CH3-Cl -> Cl-CH3)
(6) mmff_cutoff.inp [Jay L. Banks, 02-Dec-1993]
Test : MMFF cutoff schemes on small molecule
(7) mmff_gener.inp [Ryszard Czerminski, 11-May-1993]
Test : MMFF parameter reader, energy & derivatives
(8) mmff_h2o.inp [Ryszard Czerminski, 11-May-1993]
Test : MMFF parameter reader
(9) mmff_icpert.inp [Jay L. Banks, 13-Apr-94]
Files: icala.mrk
Test : internal coordinate TSM with MMFF force field
(10) mmff_pep27.inp [Thomas, 11-Feb-1995]
File : top_all22_prot_mmff.inp
(11) mmff_pert.inp [Ryszard Czerminski, 08-Sep-1994]
Files: sg.15K.punit lambda schedule file
Test : PERT command (slow growth method) with MMFF to calculate free
energy perturbation for migrating -OH group in methanol
(CH3-OH -> OH-CH3)
(12) mmff_ring.inp [Ryszard Czerminski, 11-May-1993]
Test : new MMFF ring perception code
(13) mmff_rtf.inp [Ryszard Czerminski, 11-May-1993]
Test : new RTF keywords (SINGLE, DOUBLE & TRIPLE) with ala2
(14) mmff_solanal.inp [Jay L. Banks, 13-Oct-1993]
Test : MMFF water model using solvent analysis
(15) mmff_vib.inp [Ryszard Czerminski, 30-Sep-1993]
Test : VIBRAN facility working with MMFF
New Graphics Testcases in CHARMM Version 24
As of c24b1, CHARMM graphics is substantially enhanced and a testcase
suite is also developed (test/cgrftest). Not all testcases in
cgrftest may be valid on a given system; grftest.com will select
and run the appropriate testcases based on the graphics keyword found
in pref.dat.
[ XDISPLAY GLDISPLAY NODISPLAY NOGRAPHICS APOLLO ]
grfapo.inp [Rick Venable, 05-Aug-1995]
grfgldsp.inp
grfnodsp.inp
grfnowin.inp
grfxwin.inp
Files: toph19.rtf, param19.prm, bpti.crd
Model: BPTI crystal structure
Test : exercise main graphics features
separate tests for display window and derived files
Note : for grfxwin, the env var DISPLAY must be set
PostScript, other output files are created in cgrftest
see following table for testcase/keyword matchup
--------------------------------------------------------------
Testcase Keyword in pref.dat
--------------------------------------------------------------
XDISPLAY GLDISPLAY NODISPLAY APOLLO
grfapo.inp +
grfgldsp.inp +
grfnodsp.inp + + +
grfnowin.inp +
grfxwin.inp +
--------------------------------------------------------------
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute