1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 32b1 August 15, 2005 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: CRAY XT3 Created on 4/20/ 6 at 15:41:46 by user: ?user? Maximum number of ATOMS: 240480, and RESidues: 60120 Current HEAP size: 10240000, and STACK size: 2000000 RDTITL> * CHARMM TESTCASE PME_P21.INP RDTITL> * AUTHOR: CHARLES L. BROOKS, III 20-JAN-98 RDTITL> * FILES : TOP_ALL22_PROT.INP, PAR_ALL22_PROT.INP, RDTITL> * MBCO_AU_Q0.CRD, MONO_P21.XTL, PME_P21.RST RDTITL> * TEST : DYNAMICS OF RESTRAINED MBCO IN P21 CRYSTAL USING PME AFTER RDTITL> * DELETING A HIGH-PRESSURE WATER. RDTITL> * CHARMM> CHARMM> !stream datadir.def CHARMM> bomlev -5 CHARMM> CHARMM> open unit 11 read card name top_all22_prot.inp VOPEN> Attempting to open::top_all22_prot.inp:: OPNLGU> Unit 11 opened for READONLY access to top_all22_prot.inp CHARMM> read rtf unit 11 card MAINIO> Residue topology file being read from unit 11. TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>>> JULY 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<< TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU <<<<<<<<< TITLE> * WARNING from DECODI -- Zero length string being converted to 0 RTFRDR> WARNING: Version number is NOT specified. ***** LEVEL 2 WARNING FROM ***** ***** Version number 22 not needed. ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> read rtf card append MAINIO> Residue topology file being read from unit 5. RDTITL> * SO4 ION TOPOLOGY RDTITL> * CHARMM> CHARMM> open unit 11 read card name par_all22_prot.inp VOPEN> Attempting to open::par_all22_prot.inp:: OPNLGU> Unit 11 opened for READONLY access to par_all22_prot.inp CHARMM> read param unit 11 card PARAMETER FILE BEING READ FROM UNIT 11 TITLE> *>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<<< TITLE> *>>>>>>>>>>>>>>>>>>>>>>> JULY 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<< TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU <<<<<<<<< TITLE> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> read param card append PARAMETER FILE BEING READ FROM UNIT 5 RDTITL> * SO4 PARAMETERS RDTITL> * PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> CHARMM> read sequence card MAINIO> Sequence information being read from unit 5. RDTITL> * MYOGLOBIN SEQUENCE RDTITL> * SEQRDR> 153 SEQRDR> VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HSD VAL TRP ALA SEQRDR> LYS VAL GLU ALA ASP VAL ALA GLY HSD GLY GLN ASP ILE LEU ILE SEQRDR> ARG LEU PHE LYS SER HSD PRO GLU THR LEU GLU LYS PHE ASP ARG SEQRDR> PHE LYS HSD LEU LYS THR GLU ALA GLU MET LYS ALA SER GLU ASP SEQRDR> LEU LYS LYS HSD GLY VAL THR VAL LEU THR ALA LEU GLY ALA ILE SEQRDR> LEU LYS LYS LYS GLY HSP HSD GLU ALA GLU LEU LYS PRO LEU ALA SEQRDR> GLN SER HSD ALA THR LYS HSE LYS ILE PRO ILE LYS TYR LEU GLU SEQRDR> PHE ILE SER GLU ALA ILE ILE HSD VAL LEU HSD SER ARG HSP PRO SEQRDR> GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA MET ASN LYS ALA LEU SEQRDR> GLU LEU PHE ARG LYS ASP ILE ALA ALA LYS TYR LYS GLU LEU GLY SEQRDR> TYR GLN GLY RESIDUE SEQUENCE -- 153 RESIDUES VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HSD VAL TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HSD GLY GLN ASP ILE LEU ILE ARG LEU PHE LYS SER HSD PRO GLU THR LEU GLU LYS PHE ASP ARG PHE LYS HSD LEU LYS THR GLU ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HSD GLY VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS LYS LYS GLY HSP HSD GLU ALA GLU LEU LYS PRO LEU ALA GLN SER HSD ALA THR LYS HSE LYS ILE PRO ILE LYS TYR LEU GLU PHE ILE SER GLU ALA ILE ILE HSD VAL LEU HSD SER ARG HSP PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE ALA ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY ***** Message from SEQRDR ***** THE SYSTEM CONTAINS 43 TITRATABLE GROUPS THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF HIS - 0 ASP - 7 GLU - 14 LYS - 19 TYR - 3 CHARMM> CHARMM> generate MB THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE THE PATCH 'CTER' WILL BE USED FOR THE LAST RESIDUE GENPSF> Segment 1 has been generated. Its identifier is MB. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 153 Number of atoms = 2461 Number of groups = 728 Number of bonds = 2489 Number of angles = 4532 Number of dihedrals = 6627 Number of impropers = 422 Number of cross-terms = 0 Number of HB acceptors = 226 Number of HB donors = 270 Number of NB exclusions = 0 Total charge = 4.00000 CHARMM> read sequ HEME 1 CHARMM> generate HEM NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 2 has been generated. Its identifier is HEM. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 2 Number of residues = 154 Number of atoms = 2534 Number of groups = 745 Number of bonds = 2569 Number of angles = 4676 Number of dihedrals = 6845 Number of impropers = 478 Number of cross-terms = 0 Number of HB acceptors = 234 Number of HB donors = 270 Number of NB exclusions = 0 Total charge = 2.00000 CHARMM> read sequ CO 1 CHARMM> generate CO NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 3 has been generated. Its identifier is CO. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 3 Number of residues = 155 Number of atoms = 2536 Number of groups = 746 Number of bonds = 2570 Number of angles = 4676 Number of dihedrals = 6845 Number of impropers = 478 Number of cross-terms = 0 Number of HB acceptors = 234 Number of HB donors = 270 Number of NB exclusions = 0 Total charge = 2.00000 CHARMM> read sequ TIP3 137 CHARMM> generate XTLW noangle nodihedral NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 4 has been generated. Its identifier is XTLW. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 4 Number of residues = 292 Number of atoms = 2947 Number of groups = 883 Number of bonds = 2981 Number of angles = 4813 Number of dihedrals = 6845 Number of impropers = 478 Number of cross-terms = 0 Number of HB acceptors = 371 Number of HB donors = 544 Number of NB exclusions = 0 Total charge = 2.00000 CHARMM> read sequ SO4 1 CHARMM> generate IONS NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 5 has been generated. Its identifier is IONS. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 5 Number of residues = 293 Number of atoms = 2952 Number of groups = 884 Number of bonds = 2985 Number of angles = 4819 Number of dihedrals = 6845 Number of impropers = 478 Number of cross-terms = 0 Number of HB acceptors = 375 Number of HB donors = 544 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> read sequ TIP3 200 CHARMM> generate WAT noangle nodihedral NO PATCHING WILL BE DONE ON THE FIRST RESIDUE NO PATCHING WILL BE DONE ON THE LAST RESIDUE GENPSF> Segment 6 has been generated. Its identifier is WAT. PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 6 Number of residues = 493 Number of atoms = 3552 Number of groups = 1084 Number of bonds = 3585 Number of angles = 5019 Number of dihedrals = 6845 Number of impropers = 478 Number of cross-terms = 0 Number of HB acceptors = 575 Number of HB donors = 944 Number of NB exclusions = 0 Total charge = 0.00000 CHARMM> CHARMM> open unit 11 read card name mbco_au_q0.crd VOPEN> Attempting to open::mbco_au_q0.crd:: OPNLGU> Unit 11 opened for READONLY access to mbco_au_q0.crd CHARMM> read coor card unit 11 SPATIAL COORDINATES BEING READ FROM UNIT 11 TITLE> * MBCO_AU_SDCONJ_Q0.CRD AFTER 50 SD, 150 CONJ TITLE> * ONLY PROTEIN HEAVY ATOMS FIXED. TITLE> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> crystal define monoclinic 64.180 30.840 34.690 90.00 105.84 90.00 Crystal Parameters : Crystal Type = MONO A = 64.18000 B = 30.84000 C = 34.69000 Alpha = 90.00000 Beta = 105.84000 Gamma = 90.00000 CHARMM> open unit 1 read card name mono_p21.xtl VOPEN> Attempting to open::mono_p21.xtl:: OPNLGU> Unit 1 opened for READONLY access to mono_p21.xtl CHARMM> crystal read unit 1 card CRYSTAL FILE BEING READ FROM UNIT 1 TITLE> * CRYSTAL FILE FOR MBCO (KURIYAN ET AL.). CUTOFF 20.0 ANGSTROMS. TITLE> * A,B,C,ALPHA,BETA,GAMMA = 64.180 30.840 34.690 90.00 105.84 90.00 TITLE> * TITLE> * CRYSTAL FILE FOR MBCO (KURIYAN ET AL.). CUTOFF 20.0 ANGSTROMS. TITLE> * A,B,C,ALPHA,BETA,GAMMA = 64.180 30.840 34.690 90.00 105.84 90.00 TITLE> * THERE ARE ROTATIONS FOR THIS TRANSFORMATION SET 20 Transformations have been processed. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> define prot sele segid mb .or. segid hem .or. segid co end SELRPN> 2536 atoms have been selected out of 3552 CHARMM> coor stat sele segid wat end SELRPN> 600 atoms have been selected out of 3552 STATISTICS FOR 600 SELECTED ATOMS: XMIN = -9.499310 XMAX = 37.290890 XAVE = 15.038922 YMIN = 4.612450 YMAX = 37.192190 YAVE = 21.249225 ZMIN = -13.653910 ZMAX = 26.522360 ZAVE = 7.239641 WMIN = 0.000000 WMAX = 68.726490 WAVE = 4.434708 CHARMM> coor stat sele segid xtlw end SELRPN> 411 atoms have been selected out of 3552 STATISTICS FOR 411 SELECTED ATOMS: XMIN = -7.082230 XMAX = 35.939750 XAVE = 12.413367 YMIN = -0.447230 YMAX = 42.562510 YAVE = 21.612788 ZMIN = -13.862940 ZMAX = 27.814340 ZAVE = 5.170992 WMIN = 0.000000 WMAX = 92.068040 WAVE = 10.257743 CHARMM> coor stat sele prot end SELRPN> 2536 atoms have been selected out of 3552 STATISTICS FOR 2536 SELECTED ATOMS: XMIN = -8.777440 XMAX = 36.470180 XAVE = 14.310559 YMIN = 0.484800 YMAX = 41.705750 YAVE = 21.105407 ZMIN = -12.638800 ZMAX = 27.185750 ZAVE = 6.482405 WMIN = 0.000000 WMAX = 0.000000 WAVE = 0.000000 CHARMM> image byres sele .not. prot .and. .not. type h* end - CHARMM> xcen ?xave ycen ?yave zcen ?zave RDCMND substituted energy or value "?XAVE" to "14.3106" RDCMND substituted energy or value "?YAVE" to "21.1054" RDCMND substituted energy or value "?ZAVE" to "6.48241" SELRPN> 342 atoms have been selected out of 3552 IMAGE CENTERING ON FOR SOME ATOMS CHARMM> update inbf 0 cutim 4.0 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 14.310600 21.105400 6.482410 : updating the image atom lists and remapping Transformation Atoms Groups Residues Upper-Bound 1 C001 has 18 6 6 0.00 2 C002 has 503 145 93 0.00 3 C003 has 88 24 16 4.64 4 C004 has 556 156 106 0.00 9 C009 has 0 0 0 10.01 10 C010 has 410 125 78 0.00 13 C013 has 219 58 28 0.00 15 C015 has 190 55 47 0.00 17 C017 has 0 0 0 10.26 18 C018 has 279 84 60 0.00 Total of 5815 atoms and 1737 groups and 927 residues were included CHARMM> coor stat sele segid wat end SELRPN> 600 atoms have been selected out of 3552 STATISTICS FOR 600 SELECTED ATOMS: XMIN = -9.499310 XMAX = 37.290890 XAVE = 15.038922 YMIN = 4.612450 YMAX = 37.192190 YAVE = 21.249225 ZMIN = -13.653910 ZMAX = 26.522360 ZAVE = 7.239641 WMIN = 0.000000 WMAX = 68.726490 WAVE = 4.434708 CHARMM> coor stat sele segid xtlw end SELRPN> 411 atoms have been selected out of 3552 STATISTICS FOR 411 SELECTED ATOMS: XMIN = -7.082230 XMAX = 35.939750 XAVE = 12.413367 YMIN = -0.447230 YMAX = 42.562510 YAVE = 21.612788 ZMIN = -13.862940 ZMAX = 27.814340 ZAVE = 5.170992 WMIN = 0.000000 WMAX = 92.068040 WAVE = 10.257743 CHARMM> CHARMM> !open read form unit 40 name @0pme_p21.rst CHARMM> open write form unit 41 name dyn.rst VOPEN> Attempting to open::dyn.rst:: OPNLGU> Unit 41 opened for WRITE access to dyn.rst CHARMM> dyna verlet strt nstep 10 timestep 0.001 - CHARMM> iprfrq 1000 ihtfrq 0 ieqfrq 1000 - CHARMM> iuncrd -1 iunrea -1 iunwri 41 iunvel -1 kunit -1 - CHARMM> nprint 1 nsavc 0 nsavv 0 ihbfrq 0 - CHARMM> iasors 1 iasvel 1 iscvel 0 ichecw 0 - CHARMM> twindh 10.0 twindl -10.0 ntrfrq 1000 - CHARMM> inbfrq -1 atom vatom cutnb 12.0 ctofnb 10. cdie eps 1. - CHARMM> ctonnb 9.99 vshift cutim 14.0 imgfrq 25 wmin .5 - CHARMM> ewald pmewald kappa 0.32 order 6 fftx 80 ffty 36 fftz 48 - CHARMM> spline echeck 100000.0 firstt 300. finalt 300. tstruc 200. IUNREA = -1 IUNWRI = 41 IUNOS = -1 IUNCRD = -1 IUNVEL = -1 KUNIT = -1 SELECTED IMAGES ATOMS BEING CENTERED ABOUT 14.310600 21.105400 6.482410 Total heap storage needed = 467126 Fill Ewald table: Number of points= 10000 EWXmax= 3.360000 Fill ERFC table: linear inter has rms error = 0.688344D-08 Maximum error = 0.136719D-07 Fill ERFC table: cubic spline has rms error = 0.199973D-11 Maximum error = 0.535849D-11 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSHIft BYGRoup NOEXtnd EWALd CUTNB = 12.000 CTEXNB =999.000 CTONNB = 9.990 CTOFNB = 10.000 WMIN = 0.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 PME EWALD OPTIONS: KAPPA = 0.320 QCOR = 0.000 Bspline order = 6 FFTX= 80 FFTY= 36 FFTZ= 48 Using Pub FFT Real-to-Complex FFT There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions. with mode 5 found 8267 exclusions and 6690 interactions(1-4) found 2136 group exclusions. ***** LEVEL 1 WARNING FROM ***** ***** SMALLEST UPDATE FREQUENCY IS NOT A COMMON DENOMINATOR ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 OLD NEW NSTEP 10 10 IEQFRQ 1000 1000 NTRFRQ 1000 1000 ILBFRQ 50 50 IMGFRQ 25 20 NSTEP = 10 NSAVC = 0 NSAVV = 0 ISCALE = 0 ISCVEL = 0 IASORS = 1 IASVEL = 1 ICHECW = 0 NTRFRQ = 1000 IHTFRQ = 0 IEQFRQ = 1000 NPRINT = 1 INBFRQ = -1 IHBFRQ = 0 IPRFRQ = 10 ILBFRQ = 50 IMGFRQ = 20 ISEED = 314159 ISVFRQ = 0 NCYCLE = 10 NSNOS = 10 FIRSTT = 300.000 TEMINC = 5.000 TSTRUC = 200.000 FINALT = 300.000 TWINDH = 10.000 TWINDL = -10.000 TIME STEP = 2.04548E-02 AKMA 1.00000E-03 PS NUMBER OF DEGREES OF FREEDOM = 10655 SEED FOR RANDOM NUMBER GENERATOR IS 314159 GAUSSIAN OPTION IS 1 VELOCITIES ASSIGNED AT TEMPERATURE = 400.0000 DETAILS ABOUT CENTRE OF MASS POSITION : 14.343670 21.170910 6.4225127 VELOCITY : 6.27281284E-03 6.52028255E-04 -8.70698477E-05 ANGULAR MOMENTUM : -1180.6297 -137.26170 2398.9248 KINETIC ENERGY : 0.47764377 DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers DYNA EXTERN: VDWaals ELEC HBONds ASP USER DYNA IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec DYNA EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme ---------- --------- --------- --------- --------- --------- DYNA> 0 0.00000 -2297.65453 4247.09321 -6544.74773 401.17025 DYNA PROP> 21.56327 -2290.93795 4267.24293 6.71658 -5023.17928 DYNA INTERN> 981.56293 1139.55895 115.17794 749.26926 77.21319 DYNA EXTERN> 315.37248 -4581.83937 0.00000 0.00000 0.00000 DYNA IMAGES> 145.50683 -2293.23819 0.00000 0.00000 0.00000 DYNA EWALD> 217.58729 -35303.37336 31892.45431 0.00000 0.00000 DYNA PRESS> 832.15141 2516.63478 -1727.62523 11130.90641 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 1 0.00100 -2271.85103 3951.08670 -6222.93773 373.21019 DYNA PROP> 23.10679 -2229.66700 3997.06002 42.18403 -4505.79814 DYNA INTERN> 1243.09561 1182.78092 129.77997 750.12534 76.48191 DYNA EXTERN> 312.47467 -4577.29790 0.00000 0.00000 0.00000 DYNA IMAGES> 142.00240 -2291.72524 0.00000 0.00000 0.00000 DYNA EWALD> 220.03344 -35303.37336 31892.68451 0.00000 0.00000 DYNA PRESS> 842.97486 2160.89057 -1750.09573 10018.39746 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 2 0.00200 -2227.89894 3417.28754 -5645.18649 322.78880 DYNA PROP> 25.21382 -2234.69652 3507.29330 -6.79758 -3424.44709 DYNA INTERN> 1671.02914 1302.47232 159.40197 755.89079 76.08304 DYNA EXTERN> 302.60060 -4570.43314 0.00000 0.00000 0.00000 DYNA IMAGES> 136.14652 -2289.63250 0.00000 0.00000 0.00000 DYNA EWALD> 222.50768 -35303.37336 31892.12044 0.00000 0.00000 DYNA PRESS> 791.89611 1491.06862 -1644.05141 7949.91548 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 3 0.00300 -2221.82991 3231.55775 -5453.38767 305.24521 DYNA PROP> 24.44325 -2238.09253 3327.80368 -16.26262 -2770.99062 DYNA INTERN> 1672.98939 1462.11674 184.73449 765.69136 76.28072 DYNA EXTERN> 283.06838 -4554.93263 0.00000 0.00000 0.00000 DYNA IMAGES> 128.92571 -2284.39167 0.00000 0.00000 0.00000 DYNA EWALD> 224.02631 -35303.37336 31891.47689 0.00000 0.00000 DYNA PRESS> 722.97807 1124.34902 -1500.97102 6940.14583 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 4 0.00400 -2258.41744 3481.88293 -5740.30038 328.89032 DYNA PROP> 20.58778 -2235.45133 3541.63343 22.96612 -2987.40500 DYNA INTERN> 1206.13029 1614.48661 196.18142 778.16974 77.41522 DYNA EXTERN> 256.51803 -4528.59144 0.00000 0.00000 0.00000 DYNA IMAGES> 121.91846 -2274.81909 0.00000 0.00000 0.00000 DYNA EWALD> 224.53324 -35303.37336 31891.13052 0.00000 0.00000 DYNA PRESS> 644.66495 1346.93838 -1338.38556 7698.21636 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 5 0.00500 -2287.04637 3689.75928 -5976.80564 348.52582 DYNA PROP> 17.39469 -2230.48155 3720.70335 56.56481 -3729.74736 DYNA INTERN> 830.63032 1718.29866 200.49592 791.78343 79.80216 DYNA EXTERN> 229.46065 -4494.76409 0.00000 0.00000 0.00000 DYNA IMAGES> 116.90049 -2261.83089 0.00000 0.00000 0.00000 DYNA EWALD> 224.81269 -35303.37336 31890.97838 0.00000 0.00000 DYNA PRESS> 528.13845 1958.35979 -1096.46551 9215.42926 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 6 0.00600 -2270.44570 3474.53224 -5744.97794 328.19599 DYNA PROP> 19.06041 -2229.75633 3521.69384 40.68937 -4540.31091 DYNA INTERN> 978.35319 1749.67370 208.80292 805.05156 83.65634 DYNA EXTERN> 206.53039 -4457.97536 0.00000 0.00000 0.00000 DYNA IMAGES> 114.50437 -2246.64848 0.00000 0.00000 0.00000 DYNA EWALD> 225.48150 -35303.37336 31890.96529 0.00000 0.00000 DYNA PRESS> 356.38194 2670.49200 -739.88270 10418.44152 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 7 0.00700 -2232.29814 3050.20378 -5282.50192 288.11494 DYNA PROP> 22.71511 -2233.94180 3135.12499 -1.64366 -5417.10958 DYNA INTERN> 1419.27741 1706.18499 221.02387 816.69365 89.04563 DYNA EXTERN> 187.64019 -4420.83003 0.00000 0.00000 0.00000 DYNA IMAGES> 113.63599 -2229.56897 0.00000 0.00000 0.00000 DYNA EWALD> 226.40539 -35303.37336 31891.36331 0.00000 0.00000 DYNA PRESS> 157.20404 3454.20234 -326.37050 11510.46278 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 8 0.00800 -2222.69596 2920.30699 -5143.00295 275.84520 DYNA PROP> 24.03003 -2237.28227 3014.60213 -14.58631 -6533.20972 DYNA INTERN> 1602.01268 1606.14804 225.11556 825.75848 95.86321 DYNA EXTERN> 170.21460 -4385.82618 0.00000 0.00000 0.00000 DYNA IMAGES> 112.66324 -2211.10477 0.00000 0.00000 0.00000 DYNA EWALD> 227.19026 -35303.37336 31892.33529 0.00000 0.00000 DYNA PRESS> -24.22819 4379.70134 50.30003 13265.07520 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 9 0.00900 -2251.59320 3217.02722 -5468.62041 303.87269 DYNA PROP> 22.48024 -2235.55251 3282.37581 16.04069 -7589.58066 DYNA INTERN> 1369.63829 1483.17644 211.53145 831.78798 103.81345 DYNA EXTERN> 153.52301 -4357.80212 0.00000 0.00000 0.00000 DYNA IMAGES> 111.30896 -2193.54299 0.00000 0.00000 0.00000 DYNA EWALD> 227.87018 -35303.37336 31893.44830 0.00000 0.00000 DYNA PRESS> -188.55485 5248.27528 391.45774 15438.93276 33027.51896 ---------- --------- --------- --------- --------- --------- DYNA> 10 0.01000 -2279.58439 3560.88117 -5840.46556 336.35231 DYNA PROP> 20.71337 -2231.47449 3598.31028 48.10990 -7836.99954 DYNA INTERN> 1103.40284 1375.16621 185.69897 834.88074 112.41783 DYNA EXTERN> 139.98762 -4341.93737 0.00000 0.00000 0.00000 DYNA IMAGES> 110.72668 -2180.12498 0.00000 0.00000 0.00000 DYNA EWALD> 228.73326 -35303.37336 31893.95600 0.00000 0.00000 DYNA PRESS> -375.64845 5600.31481 779.88180 16607.07348 33027.51896 ---------- --------- --------- --------- --------- --------- DYNAMC> Averages for the last 10 steps: AVER DYN: Step Time TOTEner TOTKe ENERgy TEMPerature AVER PROP: GRMS HFCTote HFCKe EHFCor VIRKe AVER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers AVER EXTERN: VDWaals ELEC HBONds ASP USER AVER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec AVER EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil AVER PRESS: VIRE VIRI PRESSE PRESSI VOLUme ---------- --------- --------- --------- --------- --------- AVER> 10 0.01000 -2252.36611 3399.45256 -5651.81867 321.10415 AVER PROP> 21.97455 -2233.63963 3464.66008 18.72647 -4933.55986 AVER INTERN> 1309.65592 1520.05046 192.27665 795.58331 87.08595 AVER EXTERN> 224.20181 -4469.03903 0.00000 0.00000 0.00000 AVER IMAGES> 120.87328 -2246.33896 0.00000 0.00000 0.00000 AVER EWALD> 225.15940 -35303.37336 31892.04589 0.00000 0.00000 AVER PRESS> 345.58069 2943.45922 -717.45829 10906.20901 33027.51896 ---------- --------- --------- --------- --------- --------- DYNAMC> RMS fluctuations for the last 10 steps: FLUC> 10 0.01000 23.45516 289.89827 308.57051 27.38310 FLUC PROP> 2.36389 2.94567 272.20733 25.98718 1755.15081 FLUC INTERN> 275.79054 181.60525 27.78164 30.25562 12.29226 FLUC EXTERN> 59.26796 84.54945 0.00000 0.00000 0.00000 FLUC IMAGES> 10.56506 38.89454 0.00000 0.00000 0.00000 FLUC EWALD> 2.46991 0.00000 1.00236 0.00000 0.00000 FLUC PRESS> 411.05221 1559.47214 853.38337 3124.42348 0.00069 ---------- --------- --------- --------- --------- --------- DRIFT/STEP (LAST-TOTAL): -7.85103692E-02 -7.85103692E-02 E AT STEP 0 : -2233.2078 -2233.2078 CORR. COEFFICIENT : -7.65542521E-02 -7.65542521E-02 WRIDYN: RESTart file was written at step 10 VCLOSE: Closing unit 41 with status "KEEP" DETAILS ABOUT CENTRE OF MASS POSITION : 14.345317 21.170910 6.4227285 VELOCITY : 9.09895087E-03 -2.06533787E-10 1.54821413E-03 ANGULAR MOMENTUM : -1057.9756 2.2991528 2201.3555 KINETIC ENERGY : 1.0228390 CHARMM> CHARMM> stop Parallel load balance (sec.): Node Eext Eint Wait Comm List Integ Total 0 0.2 0.0 0.0 0.0 0.0 1.8 2.0 1 0.2 0.0 0.0 0.0 0.0 0.0 0.2 2 0.2 0.0 0.0 0.0 0.0 0.0 0.2 3 0.2 0.0 0.0 0.0 0.0 0.0 0.2 4 0.2 0.0 0.0 0.0 0.0 0.0 0.2 5 0.2 0.0 0.0 0.0 0.0 0.0 0.2 6 0.2 0.0 0.0 0.0 0.0 0.0 0.2 7 0.2 0.0 0.0 0.0 0.0 0.0 0.2 8 0.2 0.0 0.0 0.0 0.0 0.0 0.2 9 0.2 0.0 0.0 0.0 0.0 0.0 0.2 10 0.2 0.0 0.0 0.0 0.0 0.0 0.2 11 0.2 0.0 0.0 0.0 0.0 0.0 0.2 12 0.2 0.0 0.0 0.0 0.0 0.0 0.2 13 0.2 0.0 0.0 0.0 0.0 0.0 0.2 14 0.2 0.0 0.0 0.0 0.0 0.0 0.2 15 0.2 0.0 0.0 0.0 0.0 0.0 0.2 PARALLEL> Average timing for all nodes: 16 0.2 0.0 0.0 0.0 0.0 0.1 0.3 $$$$$$ New timer profile Local node$$$$$ dynamc 3.00000 Other: 0.00000 Dynamics total 7.00000 Other: 4.00000 Total time 19.00000 Other: 12.00000 $$$$$$ Average profile $$$$$ dynamc 2.62500 Other: 0.00000 Dynamics total 7.75000 Other: 4.75000 Comm force 0.12500 Other: 0.00000 Energy time 0.18750 Other: 0.00000 Total time 18.06250 Other: 11.06250 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 106702 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL 1 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 5094720 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 19.00 SECONDS CPU TIME: ******** HOURS