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testcase

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. * 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
Top 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 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. (6) The purpose of testcases is to ensure correctness, not performance. A modern workstation should run each new testcase in 1 second or less. (7) Running new testcases with the Valgrind utility (http://valgrind.org/) is recommended to detect uninitialized variable usage and out-of-bounds array access.
Top 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."
Top 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
Top 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
Top 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
Top 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
Top 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
Top 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
Top 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]
Top 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
Top 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 + --------------------------------------------------------------