0NOTE source of yout184 server:/B/bpti/bpti4d30/bpti.9/cold.0_32.564free summaries of description/input/output of simulation ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- FILE _mdout.long ------------------------------------------------------ Amber 4.0 MIN-MD including polarization: double precision (Latest update November 1991) ------------------------------------------------------ File assignments: mdin mdout inpcrd prmtop restrt refc mdvel mden mdcrd mdinfo Here is the input file: md cont. run: at , 100K, .001x32768ps, Uncharged SC+TERM, No Water, DIELC=1, TAU &cntrl timlim = 999999., irest = 1, ibelly = 0, kform = 1, ichdna = 0, imin = 0, ipol = 0, jptres = 62, ntx = 5, ntxo = 1, ig = 77752, tempi = 100, heat = 0.0, ntb = 0, iftres = 1, nrun = 1, ntt = 1, temp0 = 100, dtemp = 999.00, tautp = 0.1, tauts = 0.1, ntp = 0, pres0 = 1.0, comp = 44.6, taup = 0.2, npscal = 0, ndfmin = 0, ntcm = 0, nscm = 0, nstlim = 32768, init = 4, ntu = 1, t = 0, dt = .001, ntc = 2, tol = 0.0005, ntf = 2, ntid = 0, ntnb = 1, nsnb = 25, idiel = 1, imgslt = 0, cut = 9.0, scnb = 2.0, scee = 2.0, dielc = 1, ntpr = 128, ntwx = 2, ntwv = 0, ntwe = 0, ntwxm = 999999, ntwvm = 999999, ntwem = 999999, ioutfm = 0, ntr = 1, ntrx = 1, ivcap = 0, fcap = 0.0, maxcyc = 2000, ncyc = 10, ntmin = 1, dx0 = 0.01, dxm = 0.5, dele = 0.0001, drms = 0.0001 &end 7 0 0 0 0 0 0 0 573 1 347 346 345 355 0.000 00.0 59.1 800.0 0 571 1 347 348 349 350 0.000 00.0 0.0 800.0 0 572 1 347 354 353 350 0.000 00.0 0.0 800.0 0 575 1 348 347 354 353 0.000 00.0 0.0 800.0 0 576 1 348 349 350 353 0.000 00.0 0.0 800.0 0 577 1 349 348 347 354 0.000 00.0 0.0 800.0 0 578 1 349 350 353 354 0.000 00.0 0.0 800.0 0 1. RESOURCE USE: NATOM = 591 NTYPES = 16 NBONH = 124 MBONA = 481 NTHETH = 199 MTHETA = 663 NPHIH = 374 MPHIA = 917 NHPARM = 0 NPARM = 0 NNB = 2565 NRES = 62 NBONA = 481 NTHETA = 663 NPHIA = 917 NUMBND = 41 NUMANG = 92 NPTRA = 53 NATYP = 19 NPHB = 20 IFBOX = 0 NMXRS = 17 IFCAP = 0 enter locmem Memory Use Allocated Used Real 650000 36386 Integer 2000000 55609 (static) Max Nonbonded Pairs: 3888782 packed 2 to a machine word pointers reset: iptres = 62 iptatm = 591 2. CONTROL DATA FOR THE RUN md cont. run: at , 100K, .001x32768ps, Uncharged SC+TERM, No Water, DIELC=1, TAU TIMLIM= 999999. IREST = 1 IBELLY= 0 KFORM = 1 ICHDNA= 0 IMIN = 0 IPOL = 0 JPTRES = 62 NTX = 5 NTXO = 1 NTCX = 0 ISEED = 77752 TEMPI = 100.00 HEAT = 0.000 NTB = 0 IFTRES= 1 BOXX = 0.000 BOXY = 0.000 BOXZ = 0.000 BETA = 0.000 NRUN = 1 NTT = 1 TEMP0 = 100.000 DTEMP = 999.000 TAUTP = 0.100 TAUTS = 0.100 NTP = 0 PRES0 = 1.000 COMP = 44.600 TAUP = 0.200 NPSCAL= 0 NDFMIN= 0 NTCM = 0 NSCM = 9999999 NSTLIM=32768 INIT = 4 NTU = 1 T = 0.000 DT = 0.00100 NTC = 2 NTCC = 0 NCONP = 0 TOL = 0.00050 NTF = 2 NTID = 0 NTN = 0 NTNB = 1 NSNB = 25 IDIEL = 1 IMGSLT= 0 RCUT = 9.000 SCNB = 2.000 SCEE = 2.000 DIELC = 1.000 NTPR = 128 NTWX = 2 NTWV = 0 NTWE = 0 NTWXM = 999999 NTWVM = 999999 NTWEM = 999999 NTPP = 0 IOUTFM= 0 NTR = 1 NTRX = 1 IVCAP = 0 NATCAP= 0 FCAP = 1.500 OTHER DATA: IFCAP = 0 MATCAP= 0 CUTCAP= 0.000 XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000 IPTRES= 0 IPTATM= 0 NSPSOL= 0 NSPSTR= 0 IPTSOL= 62 NATOM = 591 NRES = 62 %MINMD-I-MINFO, maxcyc = 2000 ncyc = 10 ntmin = 1 dx0 = 0.01000 dxm = 0.50000 dele = 0.00010 drms = 0.00010 LOADING THE PERIODIC CONSTRAINT INFORMATION 7 0.00000 0 0 0 0 0 0 0 573 1 347 346 345 355 571 1 347 348 349 350 572 1 347 354 353 350 575 1 348 347 354 353 576 1 348 349 350 353 577 1 349 348 347 354 578 1 349 350 353 354 0.00000 0.00000 1.03149 800.00000 1.00000 0.00000 0.00000 0.00000 0.00000 800.00000 1.00000 0.00000 0.00000 0.00000 0.00000 800.00000 1.00000 0.00000 0.00000 0.00000 0.00000 800.00000 1.00000 0.00000 0.00000 0.00000 0.00000 800.00000 1.00000 0.00000 0.00000 0.00000 0.00000 800.00000 1.00000 0.00000 0.00000 0.00000 0.00000 800.00000 1.00000 0.00000 3. ATOMIC COORDINATES AND VELOCITIES 4pti Tyr-35 CONS +- 0-180, Unchrgd SC & NC United Atom, 300K, Taup=.1, IDIEL=1 begin time read from input coords = 77.046 ps %MINMD-I-NRUN, beginning MD run = 1 ENTERING INTO DYNAMICS NB-UPDATE: NPAIRS = 82653 HBPAIR = 4935 571 2 19 1 347 348 349 350 571 7 0 0.08934 0.00000 0.00000 3.14159 -800.00000 0.00000 0.08934 0.99601 0.08922 0.08922 -5.30000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 5.30000 3.14159 3.19072 -800.00000 -800.00000 -800.00000 tor= 571 phi= 0.089 psi= 3.142 epw= 3.191 df= -800.000 dum= 0.000 T 571 1 0.089 3.142 3.191 -800.000 -71.379 0.000 572 3 19 1 347 354 353 350 572 7 0 0.09773 0.00000 0.00000 3.14159 -800.00000 0.00000 0.09773 0.99523 0.09758 0.09758 -5.30000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 5.30000 3.14159 3.81764 -800.00000 -800.00000 -800.00000 tor= 572 phi= 0.098 psi= 3.142 epw= 3.818 df= -800.000 dum= 0.000 T 572 1 0.098 3.142 3.818 -800.000 -78.062 0.000 573 1 9 1 347 346 345 355 573 7 0 1.03806 0.00000 0.00000 4.17308 -410.83300 -686.45192 1.03806 0.50789 0.86142 0.86142 1.00000 0.00000 0.00100 0.00000 1.03149 0.00000 1.00000 800.00000 1.00000 0.00000 0.01728 -6.10398 -6.10398 -410.83300 tor= 573 phi= 1.038 psi= 4.173 epw= 0.017 df= -6.104 dum= 0.000 T 573 1 1.038 4.173 0.017 -6.104 -5.258 0.000 575 4 17 1 348 347 354 353 575 7 0 6.23914 0.00000 0.00000 3.14159 -800.00000 0.00000 6.23914 0.99903 -0.04403 -0.04403 -2.65000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 2.65000 3.14159 0.77590 -800.00000 -800.00000 -800.00000 tor= 575 phi= 6.239 psi= 3.142 epw= 0.776 df= -800.000 dum= 0.000 T 575 1 6.239 3.142 0.776 -800.000 35.226 0.000 576 5 3 1 348 349 350 353 576 7 0 6.24461 0.00000 0.00000 3.14159 -800.00000 0.00000 6.24461 0.99926 -0.03857 -0.03857 -2.65000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 2.65000 3.14159 0.59524 -800.00000 -800.00000 -800.00000 tor= 576 phi= 6.245 psi= 3.142 epw= 0.595 df= -800.000 dum= 0.000 T 576 1 6.245 3.142 0.595 -800.000 30.855 0.000 577 6 17 1 349 348 347 354 577 7 0 6.23561 0.00000 0.00000 3.14159 -800.00000 0.00000 6.23561 0.99887 -0.04756 -0.04756 -2.65000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 2.65000 3.14159 0.90537 -800.00000 -800.00000 -800.00000 tor= 577 phi= 6.236 psi= 3.142 epw= 0.905 df= -800.000 dum= 0.000 T 577 1 6.236 3.142 0.905 -800.000 38.050 0.000 578 7 3 1 349 350 353 354 578 7 0 6.22564 0.00000 0.00000 3.14159 -800.00000 0.00000 6.22564 0.99834 -0.05752 -0.05752 -2.65000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 2.65000 3.14159 1.32430 -800.00000 -800.00000 -800.00000 tor= 578 phi= 6.226 psi= 3.142 epw= 1.324 df= -800.000 dum= 0.000 T 578 1 6.226 3.142 1.324 -800.000 46.012 0.000 DQ 1 -0.051 -0.051 0.323 158.722 163.844 0.010 0.001 NSTEP = 1 TIME(PS) = 77.047 TEMP(K) = 97.23 PRESS = 0.00 Etot = -1775.3199 EKtot = 159.2990 EPtot = -1934.6189 BOND = 64.8590 ANGLE = 98.0946 DIHED = 158.5864 1-4 NB = 109.9679 1-4 EEL = 1918.4761 NONBOND = -430.4641 NBEEL = -3822.7758 EHBOND = -31.3630 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ NB-UPDATE: NPAIRS = 83521 HBPAIR = 4965 NB-UPDATE: NPAIRS = 83332 HBPAIR = 4977 NB-UPDATE: NPAIRS = 83224 HBPAIR = 4966 NB-UPDATE: NPAIRS = 83026 HBPAIR = 4942 NB-UPDATE: NPAIRS = 83267 HBPAIR = 4942 tor= 571 phi= 0.025 psi= 3.142 epw= 0.251 df= -800.000 dum= 0.000 tor= 572 phi= 6.252 psi= 3.142 epw= 0.400 df= -800.000 dum= 0.000 T 573 128 1.028 4.173 0.063 2.988 2.488 0.000 tor= 573 phi= 1.023 psi= 4.173 epw= 0.031 df= 8.198 dum= 0.000 tor= 575 phi= 0.037 psi= 3.142 epw= 0.547 df= -800.000 dum= 0.000 tor= 576 phi= 6.260 psi= 3.142 epw= 0.220 df= -800.000 dum= 0.000 tor= 577 phi= 6.251 psi= 3.142 epw= 0.424 df= -800.000 dum= 0.000 tor= 578 phi= 0.026 psi= 3.142 epw= 0.270 df= -800.000 dum= 0.000 DQ 128 -1.531 -1.480 0.432 157.059 163.844 0.010 0.001 NSTEP = 128 TIME(PS) = 77.174 TEMP(K) = 96.84 PRESS = 0.00 Etot = -1774.1954 EKtot = 158.6610 EPtot = -1932.8564 BOND = 68.2180 ANGLE = 109.4946 DIHED = 146.6162 1-4 NB = 110.7943 1-4 EEL = 1916.9039 NONBOND = -431.7135 NBEEL = -3818.7316 EHBOND = -34.4383 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ [deleted many lines] ------------------------------------------------------------------------------ NSTEP = 32640 TIME(PS) = 109.686 TEMP(K) = 94.95 PRESS = 0.00 Etot = -1772.7474 EKtot = 155.5716 EPtot = -1928.3190 BOND = 60.7279 ANGLE = 106.4963 DIHED = 159.7351 1-4 NB = 108.8149 1-4 EEL = 1920.0933 NONBOND = -431.2624 NBEEL = -3819.9567 EHBOND = -32.9673 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ NB-UPDATE: NPAIRS = 82875 HBPAIR = 4946 NB-UPDATE: NPAIRS = 83574 HBPAIR = 4969 NB-UPDATE: NPAIRS = 83761 HBPAIR = 4993 NB-UPDATE: NPAIRS = 83832 HBPAIR = 4995 NB-UPDATE: NPAIRS = 83180 HBPAIR = 4960 RESULT OF LEAST SQUARE FIT OVER 3276 STEPS ENERGY DRIFT PER STEP = -0.000947 ETOT(AT X=0) = -1.772E+03 KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000 tor= 571 phi= 6.248 psi= 3.142 epw= 0.492 df= -800.000 dum= 0.000 tor= 572 phi= 6.273 psi= 3.142 epw= 0.043 df= -800.000 dum= 0.000 T 573 32768 1.027 4.173 0.147 4.133 3.368 0.000 tor= 573 phi= 1.071 psi= 4.173 epw= 0.624 df= -36.005 dum= 0.000 tor= 575 phi= 0.030 psi= 3.142 epw= 0.359 df= -800.000 dum= 0.000 tor= 576 phi= 0.054 psi= 3.142 epw= 1.163 df= -800.000 dum= 0.000 tor= 577 phi= 6.275 psi= 3.142 epw= 0.028 df= -800.000 dum= 0.000 tor= 578 phi= 6.252 psi= 3.142 epw= 0.389 df= -800.000 dum= 0.000 DQ 32768 11.323 0.480 -0.319 169.237 163.844 0.010 0.001 NSTEP = 32768 TIME(PS) = 109.814 TEMP(K) = 102.76 PRESS = 0.00 Etot = -1773.8059 EKtot = 168.3589 EPtot = -1942.1648 BOND = 56.0046 ANGLE = 105.6727 DIHED = 148.1808 1-4 NB = 112.5951 1-4 EEL = 1929.0287 NONBOND = -430.1704 NBEEL = -3830.7533 EHBOND = -32.7230 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ RESULT OF LEAST SQUARE FIT OVER 8 STEPS ENERGY DRIFT PER STEP = -0.106761 ETOT(AT X=0) = -1.773E+03 KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000 %MD-I-AVERAGES1, for the last 32768 steps NSTEP = 32768 TIME(PS) = 109.814 TEMP(K) = 100.02 PRESS = 0.00 Etot = -1773.6630 EKtot = 163.8786 EPtot = -1937.5417 BOND = 56.7051 ANGLE = 105.9885 DIHED = 149.5984 1-4 NB = 110.3315 1-4 EEL = 1919.8348 NONBOND = -430.8898 NBEEL = -3817.1177 EHBOND = -31.9926 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ %MD-I-AVERAGES2, RMS fluctuations NSTEP = 32768 TIME(PS) = 109.814 TEMP(K) = 2.92 PRESS = 0.00 Etot = 1.5728 EKtot = 4.7777 EPtot = 5.2054 BOND = 3.9232 ANGLE = 4.2526 DIHED = 5.0325 1-4 NB = 2.6955 1-4 EEL = 4.8059 NONBOND = 3.7662 NBEEL = 7.7467 EHBOND = 1.1131 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ Routine Sec % -------------------------- Pairlist 556.55 1.35 Nonbond 32698.63 79.11 Bond 189.94 0.46 Angle 865.74 2.09 Dihedral 4789.64 11.59 Shake 256.70 0.62 Pol. der 0.00 0.00 Efielde 0.00 0.00 Indip 0.00 0.00 Matmul 0.00 0.00 Other 1976.48 4.78 -------------------------- Total 41333.68 11.48 Hours ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- FILE _mdttyout.long Amber 4.0 united atom _ dynamics simulation md cont. run: at , 100K, .001x32768ps, Uncharged SC+TERM, No Water, DIELC=1, TAUTP=0.1, CM out 4pti Tyr-35 CONS +- 0-180, Unchrgd SC & NC United Atom, 300K, Taup=.1, IDIEL=1 ../Run.test_32.564free -f -c ../cold.0/cold.0_10x/_mdrestrt.long -p ../equil.0/_prmtop trial=0 start_time=0 tempi=100 temp0=100 ntx=5 init=4 irest=1 t=100 tautp=0.1 dt=.001 ntpr=128 nstlim=32768 removing old output files.. MINMD: No errors detected WHOPPEE, we're done (or we should be :-^) ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- FILE mdin md cont. run: at , 100K, .001x32768ps, Uncharged SC+TERM, No Water, DIELC=1, TAUTP=0.1, CM out &cntrl timlim = 999999., irest = 1, ibelly = 0, kform = 1, ichdna = 0, imin = 0, ipol = 0, jptres = 62, ntx = 5, ntxo = 1, ig = 77752, tempi = 100, heat = 0.0, ntb = 0, iftres = 1, nrun = 1, ntt = 1, temp0 = 100, dtemp = 999.00, tautp = 0.1, tauts = 0.1, ntp = 0, pres0 = 1.0, comp = 44.6, taup = 0.2, npscal = 0, ndfmin = 0, ntcm = 0, nscm = 0, nstlim = 32768, init = 4, ntu = 1, t = 0, dt = .001, ntc = 2, tol = 0.0005, ntf = 2, ntid = 0, ntnb = 1, nsnb = 25, idiel = 1, imgslt = 0, cut = 9.0, scnb = 2.0, scee = 2.0, dielc = 1, ntpr = 128, ntwx = 2, ntwv = 0, ntwe = 0, ntwxm = 999999, ntwvm = 999999, ntwem = 999999, ioutfm = 0, ntr = 1, ntrx = 1, ivcap = 0, fcap = 0.0, maxcyc = 2000, ncyc = 10, ntmin = 1, dx0 = 0.01, dxm = 0.5, dele = 0.0001, drms = 0.0001 &end 7 0 0 0 0 0 0 0 573 1 347 346 345 355 0.000 00.0 59.1 800.0 0 571 1 347 348 349 350 0.000 00.0 0.0 800.0 0 572 1 347 354 353 350 0.000 00.0 0.0 800.0 0 575 1 348 347 354 353 0.000 00.0 0.0 800.0 0 576 1 348 349 350 353 0.000 00.0 0.0 800.0 0 577 1 349 348 347 354 0.000 00.0 0.0 800.0 0 578 1 349 350 353 354 0.000 00.0 0.0 800.0 0 ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- FILE mdinfo NSTEP = 32768 TIME(PS) = 109.814 TEMP(K) = 102.76 PRESS = 0.00 Etot = -1773.8059 EKtot = 168.3589 EPtot = -1942.1648 BOND = 56.0046 ANGLE = 105.6727 DIHED = 148.1808 1-4 NB = 112.5951 1-4 EEL = 1929.0287 NONBOND = -430.1704 NBEEL = -3830.7533 EHBOND = -32.7230 CONSTRAINT = 0.0000 ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- John Rupley rupley@u.arizona.edu -or- jar@rupley.com 30 Calle Belleza, Tucson AZ 85716 - (520) 325-4533; fax - (520) 325-4991 Dept. Biochemistry & Molecular Biophysics, Univ. Arizona, Tucson AZ 85721