0NOTE exam1.data from y4.8.x10.2[184,], in .../bpti.9/S/.Data exam date: March 13, 1997 ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ADDED ON: Sat Oct 30 11:55:46 MST 2004 scr10.s:[240,] "y4.8.x10.2<-matrix(scan(\"test.40_800_.1_2.dihedrals\"),ncol=1024, byrow=T)" run_anal2:anal2 -t tor -l /user2/display/exe/lists/list.dihedrals.atoms -f 1024 -p 1024 -n ../testnoepw.40_800_128_512/mdcrd |tr -s " " "\012"|sed 1,2d >testnoepw.40_800_128_512.dihedrals INFORMATION ON RUN: [date or run: May 8 1994] ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- directory of files in this file: /B/bpti/bpti4d30/bpti.9/test.40_800_.1_2 ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- _mdttyout.long Amber 4.0 united atom _ dynamics simulation md cont. run: at , 100K, .001x2048ps, 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.40_800_2 -f -c ../test.40_800_1_16/_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=8 nstlim=2048 removing old output files.. MINMD: No errors detected WHOPPEE, we're done (or we should be :-^) ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- mdin md cont. run: at , 100K, .001x2048ps, 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 = 2048, 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 = 8, 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 8 0 0 0 0 0 0 0 564 1 345 346 347 348 0.128 40.0 45.2 800.0 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 ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- _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, .001x2048ps, Uncharged SC+TERM, No Water, DIELC=1, TAUT &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 = 2048, 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 = 8, 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 8 0 0 0 0 0 0 0 564 1 345 346 347 348 0.128 40.0 45.2 800.0 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, .001x2048ps, Uncharged SC+TERM, No Water, DIELC=1, TAUT 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= 2048 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 = 8 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 8 0.00000 0 0 0 0 0 0 0 564 1 345 346 347 348 573 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 0.12800 0.69813 0.78889 800.00000 1.00000 0.00000 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 = 97.526 ps %MINMD-I-NRUN, beginning MD run = 1 ENTERING INTO DYNAMICS NB-UPDATE: NPAIRS = 82499 HBPAIR = 4925 564 1 8 1 345 346 347 348 564 8 0 0.77783 0.04907 0.04909 3.96474 -543.93499 -586.62998 0.77783 0.71244 0.70173 0.70173 0.00000 0.00000 0.00100 0.12800 0.78889 0.69813 1.00000 800.00000 0.00000 0.00000 0.82130 51.64501 51.64501 -543.93499 tor= 564 phi= 0.778 psi= 3.965 epw= 0.821 df= 51.645 dum= 0.049 T 564 1 0.778 3.965 0.821 51.645 36.241 0.049 571 3 19 1 347 348 349 350 571 8 0 0.00393 0.00000 0.00000 3.14159 -800.00000 0.00000 0.00393 0.99999 0.00393 0.00393 -5.30000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 5.30000 3.14159 0.00616 -800.00000 -800.00000 -800.00000 tor= 571 phi= 0.004 psi= 3.142 epw= 0.006 df= -800.000 dum= 0.000 T 571 1 0.004 3.142 0.006 -800.000 -3.140 0.000 572 4 19 1 347 354 353 350 572 8 0 6.26974 0.00000 0.00000 3.14159 -800.00000 0.00000 6.26974 0.99991 -0.01345 -0.01345 -5.30000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 5.30000 3.14159 0.07234 -800.00000 -800.00000 -800.00000 tor= 572 phi= 6.270 psi= 3.142 epw= 0.072 df= -800.000 dum= 0.000 T 572 1 6.270 3.142 0.072 -800.000 10.758 0.000 573 2 9 1 347 346 345 355 573 8 0 1.01174 0.00000 0.00000 4.17308 -410.83300 -686.45192 1.01174 0.53039 0.84775 0.84775 1.00000 0.00000 0.00100 0.00000 1.03149 0.00000 1.00000 800.00000 1.00000 0.00000 0.15608 18.64008 18.64008 -410.83300 tor= 573 phi= 1.012 psi= 4.173 epw= 0.156 df= 18.640 dum= 0.000 T 573 1 1.012 4.173 0.156 18.640 15.802 0.000 575 5 17 1 348 347 354 353 575 8 0 0.02282 0.00000 0.00000 3.14159 -800.00000 0.00000 0.02282 0.99974 0.02282 0.02282 -2.65000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 2.65000 3.14159 0.20837 -800.00000 -800.00000 -800.00000 tor= 575 phi= 0.023 psi= 3.142 epw= 0.208 df= -800.000 dum= 0.000 T 575 1 0.023 3.142 0.208 -800.000 -18.258 0.000 576 6 3 1 348 349 350 353 576 8 0 0.00573 0.00000 0.00000 3.14159 -800.00000 0.00000 0.00573 0.99998 0.00573 0.00573 -2.65000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 2.65000 3.14159 0.01312 -800.00000 -800.00000 -800.00000 tor= 576 phi= 0.006 psi= 3.142 epw= 0.013 df= -800.000 dum= 0.000 T 576 1 0.006 3.142 0.013 -800.000 -4.581 0.000 577 7 17 1 349 348 347 354 577 8 0 6.26474 0.00000 0.00000 3.14159 -800.00000 0.00000 6.26474 0.99983 -0.01844 -0.01844 -2.65000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 2.65000 3.14159 0.13608 -800.00000 -800.00000 -800.00000 tor= 577 phi= 6.265 psi= 3.142 epw= 0.136 df= -800.000 dum= 0.000 T 577 1 6.265 3.142 0.136 -800.000 14.755 0.000 578 8 3 1 349 350 353 354 578 8 0 6.28231 0.00000 0.00000 3.14159 -800.00000 0.00000 6.28231 1.00000 -0.00088 -0.00088 -2.65000 0.00000 0.00100 0.00000 0.00000 0.00000 1.00000 800.00000 2.65000 3.14159 0.00031 -800.00000 -800.00000 -800.00000 tor= 578 phi= 6.282 psi= 3.142 epw= 0.000 df= -800.000 dum= 0.000 T 578 1 6.282 3.142 0.000 -800.000 0.703 0.000 DQ 1 0.122 0.122 -0.695 176.086 163.844 0.010 0.001 NSTEP = 1 TIME(PS) = 97.527 TEMP(K) = 107.26 PRESS = 0.00 Etot = -1765.9611 EKtot = 175.7339 EPtot = -1941.6950 BOND = 37.5703 ANGLE = 99.3169 DIHED = 144.4640 1-4 NB = 109.5063 1-4 EEL = 1920.9705 NONBOND = -420.5618 NBEEL = -3801.4769 EHBOND = -31.4843 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ T 564 8 0.858 4.099 3.995 105.616 79.579 0.242 tor= 564 phi= 0.957 psi= 4.198 epw= 3.902 df= 96.519 dum= 0.383 tor= 571 phi= 6.273 psi= 3.142 epw= 0.044 df= -800.000 dum= 0.000 tor= 572 phi= 6.266 psi= 3.142 epw= 0.115 df= -800.000 dum= 0.000 tor= 573 phi= 0.947 psi= 4.173 epw= 2.839 df= 82.947 dum= 0.000 tor= 575 phi= 6.243 psi= 3.142 epw= 0.637 df= -800.000 dum= 0.000 tor= 576 phi= 6.237 psi= 3.142 epw= 0.871 df= -800.000 dum= 0.000 tor= 577 phi= 0.054 psi= 3.142 epw= 1.164 df= -800.000 dum= 0.000 tor= 578 phi= 0.061 psi= 3.142 epw= 1.508 df= -800.000 dum= 0.000 DQ 8 1.115 0.993 -0.949 181.022 163.844 0.010 0.001 NSTEP = 8 TIME(PS) = 97.534 TEMP(K) = 110.13 PRESS = 0.00 Etot = -1749.0268 EKtot = 180.4429 EPtot = -1929.4697 BOND = 40.0024 ANGLE = 97.4136 DIHED = 160.4402 1-4 NB = 108.8648 1-4 EEL = 1921.4675 NONBOND = -420.7202 NBEEL = -3805.6430 EHBOND = -31.2949 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ ....... ------------------------------------------------------------------------------ RESULT OF LEAST SQUARE FIT OVER 204 STEPS ENERGY DRIFT PER STEP = 0.489728 ETOT(AT X=0) = -1.498E+03 KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000 T 564 2048 0.533 3.812 7.957 225.872 109.431 -0.170 tor= 564 phi= 0.707 psi= 3.930 epw= 2.689 df= 100.911 dum= 0.000 tor= 571 phi= 6.217 psi= 3.142 epw= 1.758 df= -800.000 dum= 0.000 tor= 572 phi= 6.264 psi= 3.142 epw= 0.153 df= -800.000 dum= 0.000 tor= 573 phi= 0.946 psi= 4.173 epw= 2.925 df= 84.269 dum= 0.000 tor= 575 phi= 6.237 psi= 3.142 epw= 0.861 df= -800.000 dum= 0.000 tor= 576 phi= 0.029 psi= 3.142 epw= 0.346 df= -800.000 dum= 0.000 tor= 577 phi= 0.097 psi= 3.142 epw= 3.741 df= -800.000 dum= 0.000 tor= 578 phi= 0.023 psi= 3.142 epw= 0.218 df= -800.000 dum= 0.000 DQ 2048 3708.625 10.518 -4.423 293.789 163.844 0.010 0.001 NSTEP = 2048 TIME(PS) = 99.574 TEMP(K) = 178.97 PRESS = 0.00 Etot = -1417.4924 EKtot = 293.2390 EPtot = -1710.7313 BOND = 82.8048 ANGLE = 206.9336 DIHED = 203.4739 1-4 NB = 120.9884 1-4 EEL = 1905.6957 NONBOND = -416.3123 NBEEL = -3783.1244 EHBOND = -31.1911 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ RESULT OF LEAST SQUARE FIT OVER 8 STEPS ENERGY DRIFT PER STEP = 2.678844 ETOT(AT X=0) = -1.438E+03 KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000 %MD-I-AVERAGES1, for the last 2048 steps NSTEP = 2048 TIME(PS) = 99.574 TEMP(K) = 210.54 PRESS = 0.00 Etot = -1358.3441 EKtot = 344.9576 EPtot = -1703.3017 BOND = 81.6165 ANGLE = 199.7325 DIHED = 212.5959 1-4 NB = 118.0669 1-4 EEL = 1912.5976 NONBOND = -411.2061 NBEEL = -3786.7919 EHBOND = -29.9132 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ %MD-I-AVERAGES2, RMS fluctuations NSTEP = 2048 TIME(PS) = 99.574 TEMP(K) = 36.56 PRESS = 0.00 Etot = 113.3404 EKtot = 59.9082 EPtot = 75.1979 BOND = 22.1794 ANGLE = 37.2381 DIHED = 32.0254 1-4 NB = 8.5302 1-4 EEL = 9.4736 NONBOND = 8.6675 NBEEL = 14.9970 EHBOND = 1.5706 CONSTRAINT = 0.0000 ------------------------------------------------------------------------------ Routine Sec % -------------------------- Pairlist 34.80 1.33 Nonbond 2015.03 77.24 Bond 12.60 0.48 Angle 55.63 2.13 Dihedral 301.98 11.58 Shake 15.93 0.61 Pol. der 0.00 0.00 Efielde 0.00 0.00 Indip 0.00 0.00 Matmul 0.00 0.00 Other 172.88 6.63 -------------------------- Total 2608.85 0.72 Hours 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