CHARMM c30b1 testcase.doc



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                            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



File: Testcase ]-[ Node: Overview
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                    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.



File: Testcase ]-[ Node: Instruction
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                            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."



File: Testcase ]-[ Node: C20TEST
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                          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



File: Testcase ]-[ Node: C22TEST
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                  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



File: Testcase ]-[ Node: C23TEST
Up: Top -=- Previous: C22TEST -=- Next: C24TEST\n


                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



File: Testcase ]-[ Node: C24TEST
Up: Top -=- Previous: C23TEST -=- Next: C25TEST\n


                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



File: Testcase ]-[ Node: C25TEST
Up: Top -=- Previous: C24TEST -=- Next: C26TEST\n


                    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



File: Testcase ]-[ Node: C26TEST
Up: Top -=- Previous: C25TEST -=- Next: NBONDTEST\n


                    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



File: Testcase ]-[ Node: NBONDTEST
Up: Top -=- Previous: C25TEST -=- Next: MMFFTEST\n


                    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]



File: Testcase ]-[ Node: MMFFTEST
Up: Top -=- Previous: NBONDTEST -=- Next: GRAFTEST\n


                   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



File: Testcase ]-[ Node: GRAFTEST
Up: Top -=- Previous: C24TEST -=- Next: Top\n


              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         +
    --------------------------------------------------------------


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