possible FAILURE: check mdout.dhfr.noboxinfo.dif /home/makoto/amber12/test/dhfr 1,20d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < [-O]verwriting output < File Assignments: < Here is the input file: < short minimization < &cntrl < ntx=7, irest=1, < ntc=2, ntf=2, tol=0.0000001, < imin=1, maxcyc=5, < ntpr=1, ntwr=10000, < / < &ewald < nfft1 = 72, nfft2 = 60, nfft3 = 54, < / < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting new box info from bottom of inpcrd --------------------------------------- possible FAILURE: check textmd.rst7.dif /home/makoto/amber12/test/nc_restart/MD_ncrestart_write --------------------------------------- possible FAILURE: check textmin.rst7.dif /home/makoto/amber12/test/nc_restart/Min_ncrestart_write --------------------------------------- possible FAILURE: check md.rst7.dif /home/makoto/amber12/test/nc_restart/refMD_ncrestart --------------------------------------- possible FAILURE: check md.out.dif /home/makoto/amber12/test/nc_restart/refMD_ncrestart 1,174d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < [-O]verwriting output < File Assignments: < Here is the input file: < Ala2 explicit solvent MD with netcdf restart ref coords < &cntrl < imin = 0, nstlim = 100, dt=0.001, < ntx = 5, irest = 1, ig = 1, ntxo = 1, < ntwx = 50, ioutfm = 1, ntpr = 10, ntwr = 50000, < iwrap = 0, nscm = 0, < ntc = 2, ntf = 2, ntb = 1, cut = 8.0, < ntt = 1, tautp = 5.0, temp0 = 300.0, tempi = 300.0, < ntp = 0, taup = 5.0, < ntr = 1, restraintmask = ':1-3@C,CA,N', restraint_wt = 5.0, < &end < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting new box info from bottom of inpcrd < NATOM = 2101 NTYPES = 9 NBONH = 2091 MBONA = 9 < NTHETH = 25 MTHETA = 11 NPHIH = 43 MPHIA = 24 < NHPARM = 0 NPARM = 0 NNB = 2871 NRES = 696 < NBONA = 9 NTHETA = 11 NPHIA = 24 NUMBND = 10 < NUMANG = 16 NPTRA = 19 NATYP = 9 NPHB = 1 < IFBOX = 2 NMXRS = 10 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < BOX TYPE: TRUNCATED OCTAHEDRON < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < ACE < General flags: < imin = 0, nmropt = 0 < Nature and format of input: < ntx = 5, irest = 1, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 10, ntrx = 1, ntwr = 50000 < iwrap = 0, ntwx = 50, ntwv = 0, ntwe = 0 < ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 1, igb = 0, nsnb = 25 < ipol = 0, gbsa = 0, iesp = 0 < dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 < Frozen or restrained atoms: < ibelly = 0, ntr = 1 < restraint_wt = 5.00000 < Molecular dynamics: < nstlim = 100, nscm = 0, nrespa = 1 < t = 0., dt = 0.00100, vlimit = 20.00000 < Berendsen (weak-coupling) temperature regulation: < temp0 = 300.00000, tempi = 300.00000, tautp = 5.00000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0.00001 < Ewald parameters: < verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 < vdwmeth = 1, eedmeth = 1, netfrc = 1 < Box X = 30.264 Box Y = 30.264 Box Z = 30.264 < Alpha = 109.471 Beta = 109.471 Gamma = 109.471 < NFFT1 = 30 NFFT2 = 30 NFFT3 = 30 < Cutoff= 8.000 Tol =0.100E-4 < Ewald Coefficient = 0.34864 < Interpolation order = 4 < LOADING THE CONSTRAINED ATOMS AS GROUPS < 5. REFERENCE ATOM COORDINATES < ACE < Mask :1-3@C,CA,N; matches 5 atoms < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < ACE < begin time read from input coords = 30.000 ps < Number of triangulated 3-point waters found: 693 < Sum of charges from parm topology file = 0. < Forcing neutrality... < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < --------------------------------------------------- < APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION < using 5000.0 points per unit in tabled values < TESTING RELATIVE ERROR over r ranging from 0. to cutoff < --------------------------------------------------- < NSTEP = 10 TIME(PS) = 30.010 TEMP(K) = 300.65 PRESS = 0. < Etot = -5388.6195 EKtot = 1258.2287 EPtot = -6646.8482 < BOND = 1.3338 ANGLE = 6.0071 DIHED = 11.5248 < 1-4 NB = 2.1583 1-4 EEL = 47.5443 VDWAALS = 1002.6569 < EELEC = -7718.1558 EHBOND = 0. RESTRAINT = 0.0824 < EAMBER (non-restraint) = -6646.9306 < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 30.020 TEMP(K) = 301.24 PRESS = 0. < Etot = -5388.6367 EKtot = 1260.7094 EPtot = -6649.3461 < BOND = 1.9402 ANGLE = 6.6637 DIHED = 11.4672 < 1-4 NB = 2.9022 1-4 EEL = 46.2305 VDWAALS = 978.6898 < EELEC = -7697.4551 EHBOND = 0. RESTRAINT = 0.2154 < EAMBER (non-restraint) = -6649.5615 < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 30.030 TEMP(K) = 303.16 PRESS = 0. < Etot = -5388.5832 EKtot = 1268.7424 EPtot = -6657.3256 < BOND = 1.6061 ANGLE = 6.7068 DIHED = 10.9269 < 1-4 NB = 2.6221 1-4 EEL = 46.9387 VDWAALS = 957.8851 < EELEC = -7684.3172 EHBOND = 0. RESTRAINT = 0.3061 < EAMBER (non-restraint) = -6657.6317 < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 30.040 TEMP(K) = 301.08 PRESS = 0. < Etot = -5388.5445 EKtot = 1260.0271 EPtot = -6648.5716 < BOND = 1.0083 ANGLE = 8.4078 DIHED = 11.7111 < 1-4 NB = 3.5085 1-4 EEL = 46.3303 VDWAALS = 959.5580 < EELEC = -7679.5855 EHBOND = 0. RESTRAINT = 0.4899 < EAMBER (non-restraint) = -6649.0615 < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 30.050 TEMP(K) = 304.32 PRESS = 0. < Etot = -5388.7438 EKtot = 1273.5877 EPtot = -6662.3315 < BOND = 3.1240 ANGLE = 7.4733 DIHED = 10.3652 < 1-4 NB = 2.4608 1-4 EEL = 45.3944 VDWAALS = 959.3425 < EELEC = -7691.0656 EHBOND = 0. RESTRAINT = 0.5738 < EAMBER (non-restraint) = -6662.9053 < ------------------------------------------------------------------------------ < NSTEP = 60 TIME(PS) = 30.060 TEMP(K) = 301.70 PRESS = 0. < Etot = -5388.7840 EKtot = 1262.6427 EPtot = -6651.4267 < BOND = 3.0343 ANGLE = 6.8505 DIHED = 10.7569 < 1-4 NB = 2.4641 1-4 EEL = 44.2052 VDWAALS = 956.4410 < EELEC = -7675.6562 EHBOND = 0. RESTRAINT = 0.4775 < EAMBER (non-restraint) = -6651.9043 < ------------------------------------------------------------------------------ < NSTEP = 70 TIME(PS) = 30.070 TEMP(K) = 298.70 PRESS = 0. < Etot = -5388.6712 EKtot = 1250.0868 EPtot = -6638.7580 < BOND = 1.6225 ANGLE = 10.0286 DIHED = 10.3518 < 1-4 NB = 1.8439 1-4 EEL = 46.4656 VDWAALS = 961.2807 < EELEC = -7670.6742 EHBOND = 0. RESTRAINT = 0.3231 < EAMBER (non-restraint) = -6639.0811 < ------------------------------------------------------------------------------ < NSTEP = 80 TIME(PS) = 30.080 TEMP(K) = 306.61 PRESS = 0. < Etot = -5388.8196 EKtot = 1283.1543 EPtot = -6671.9740 < BOND = 2.4624 ANGLE = 8.0833 DIHED = 10.9471 < 1-4 NB = 2.4579 1-4 EEL = 44.9431 VDWAALS = 959.3373 < EELEC = -7700.4781 EHBOND = 0. RESTRAINT = 0.2730 < EAMBER (non-restraint) = -6672.2470 < ------------------------------------------------------------------------------ < NSTEP = 90 TIME(PS) = 30.090 TEMP(K) = 297.12 PRESS = 0. < Etot = -5388.6557 EKtot = 1243.4673 EPtot = -6632.1230 < BOND = 3.2495 ANGLE = 5.4522 DIHED = 11.3794 < 1-4 NB = 2.7244 1-4 EEL = 48.1117 VDWAALS = 953.9028 < EELEC = -7657.1643 EHBOND = 0. RESTRAINT = 0.2212 < EAMBER (non-restraint) = -6632.3442 < ------------------------------------------------------------------------------ < NSTEP = 100 TIME(PS) = 30.100 TEMP(K) = 298.94 PRESS = 0. < Etot = -5388.7538 EKtot = 1251.0547 EPtot = -6639.8084 < BOND = 0.9590 ANGLE = 5.2172 DIHED = 10.1933 < 1-4 NB = 3.4539 1-4 EEL = 49.6354 VDWAALS = 951.5310 < EELEC = -7661.0550 EHBOND = 0. RESTRAINT = 0.2567 < EAMBER (non-restraint) = -6640.0651 < ------------------------------------------------------------------------------ < A V E R A G E S O V E R 100 S T E P S < NSTEP = 100 TIME(PS) = 30.100 TEMP(K) = 301.81 PRESS = 0. < Etot = -5388.6700 EKtot = 1263.0885 EPtot = -6651.7585 < BOND = 2.1803 ANGLE = 7.1867 DIHED = 10.9925 < 1-4 NB = 2.5958 1-4 EEL = 46.4714 VDWAALS = 966.2701 < EELEC = -7687.7663 EHBOND = 0. RESTRAINT = 0.3111 < EAMBER (non-restraint) = -6652.0696 < ------------------------------------------------------------------------------ < R M S F L U C T U A T I O N S < NSTEP = 100 TIME(PS) = 30.100 TEMP(K) = 3.38 PRESS = 0. < Etot = 0.1016 EKtot = 14.1385 EPtot = 14.1510 < BOND = 0.8228 ANGLE = 1.1674 DIHED = 0.4967 < 1-4 NB = 0.4585 1-4 EEL = 1.3497 VDWAALS = 16.0422 < EELEC = 23.8451 EHBOND = 0. RESTRAINT = 0.1547 < EAMBER (non-restraint) = 13.9963 < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --------------------------------------- possible FAILURE: check md.out.dif /home/makoto/amber12/test/nc_restart/restartMD.ntx5 1,156d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < [-O]verwriting output < File Assignments: < Here is the input file: < Ala2 explicit solvent MD using netcdf restart < &cntrl < imin = 0, nstlim = 100, dt=0.001, < ntx = 5, irest = 1, ig = 1, ntxo = 1, < ntwx = 50, ioutfm = 1, ntpr = 10, ntwr = 50000, < iwrap = 0, nscm = 0, < ntc = 2, ntf = 2, ntb = 1, cut = 8.0, < ntt = 1, tautp = 5.0, temp0 = 300.0, tempi = 300.0, < ntp = 0, taup = 5.0, < &end < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting box info from netcdf restart file < NATOM = 2101 NTYPES = 9 NBONH = 2091 MBONA = 9 < NTHETH = 25 MTHETA = 11 NPHIH = 43 MPHIA = 24 < NHPARM = 0 NPARM = 0 NNB = 2871 NRES = 696 < NBONA = 9 NTHETA = 11 NPHIA = 24 NUMBND = 10 < NUMANG = 16 NPTRA = 19 NATYP = 9 NPHB = 1 < IFBOX = 2 NMXRS = 10 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < BOX TYPE: TRUNCATED OCTAHEDRON < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < ACE < General flags: < imin = 0, nmropt = 0 < Nature and format of input: < ntx = 5, irest = 1, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 10, ntrx = 1, ntwr = 50000 < iwrap = 0, ntwx = 50, ntwv = 0, ntwe = 0 < ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 1, igb = 0, nsnb = 25 < ipol = 0, gbsa = 0, iesp = 0 < dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 < Frozen or restrained atoms: < ibelly = 0, ntr = 0 < Molecular dynamics: < nstlim = 100, nscm = 0, nrespa = 1 < t = 0., dt = 0.00100, vlimit = 20.00000 < Berendsen (weak-coupling) temperature regulation: < temp0 = 300.00000, tempi = 300.00000, tautp = 5.00000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0.00001 < Ewald parameters: < verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 < vdwmeth = 1, eedmeth = 1, netfrc = 1 < Box X = 30.264 Box Y = 30.264 Box Z = 30.264 < Alpha = 109.471 Beta = 109.471 Gamma = 109.471 < NFFT1 = 30 NFFT2 = 30 NFFT3 = 30 < Cutoff= 8.000 Tol =0.100E-4 < Ewald Coefficient = 0.34864 < Interpolation order = 4 < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < ACE < begin time read from input coords = 30.100 ps < Number of triangulated 3-point waters found: 693 < Sum of charges from parm topology file = 0. < Forcing neutrality... < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < --------------------------------------------------- < APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION < using 5000.0 points per unit in tabled values < TESTING RELATIVE ERROR over r ranging from 0. to cutoff < --------------------------------------------------- < NSTEP = 10 TIME(PS) = 30.110 TEMP(K) = 309.18 PRESS = 0. < Etot = -5388.8274 EKtot = 1293.9351 EPtot = -6682.7626 < BOND = 1.7801 ANGLE = 8.6834 DIHED = 11.1151 < 1-4 NB = 3.7189 1-4 EEL = 51.2569 VDWAALS = 940.6309 < EELEC = -7699.9480 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 30.120 TEMP(K) = 309.35 PRESS = 0. < Etot = -5388.9135 EKtot = 1294.6584 EPtot = -6683.5719 < BOND = 0.8663 ANGLE = 6.7890 DIHED = 10.4018 < 1-4 NB = 3.8853 1-4 EEL = 51.5333 VDWAALS = 933.5374 < EELEC = -7690.5850 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 30.130 TEMP(K) = 300.10 PRESS = 0. < Etot = -5388.8761 EKtot = 1255.9371 EPtot = -6644.8132 < BOND = 2.0187 ANGLE = 4.2116 DIHED = 11.3855 < 1-4 NB = 3.5568 1-4 EEL = 48.9769 VDWAALS = 950.4665 < EELEC = -7665.4292 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 30.140 TEMP(K) = 295.85 PRESS = 0. < Etot = -5388.9431 EKtot = 1238.1207 EPtot = -6627.0637 < BOND = 3.1356 ANGLE = 4.9277 DIHED = 10.7132 < 1-4 NB = 3.1349 1-4 EEL = 47.6618 VDWAALS = 976.8520 < EELEC = -7673.4889 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 30.150 TEMP(K) = 298.13 PRESS = 0. < Etot = -5388.8546 EKtot = 1247.6735 EPtot = -6636.5281 < BOND = 1.2371 ANGLE = 6.1832 DIHED = 10.9671 < 1-4 NB = 2.7025 1-4 EEL = 46.6935 VDWAALS = 981.9832 < EELEC = -7686.2946 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 60 TIME(PS) = 30.160 TEMP(K) = 302.45 PRESS = 0. < Etot = -5388.9290 EKtot = 1265.7650 EPtot = -6654.6940 < BOND = 2.4565 ANGLE = 6.6230 DIHED = 10.9556 < 1-4 NB = 2.2331 1-4 EEL = 46.8286 VDWAALS = 981.7284 < EELEC = -7705.5191 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 70 TIME(PS) = 30.170 TEMP(K) = 306.13 PRESS = 0. < Etot = -5389.0270 EKtot = 1281.1679 EPtot = -6670.1949 < BOND = 3.5303 ANGLE = 10.6059 DIHED = 10.8959 < 1-4 NB = 2.6663 1-4 EEL = 45.4722 VDWAALS = 987.4684 < EELEC = -7730.8338 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 80 TIME(PS) = 30.180 TEMP(K) = 304.39 PRESS = 0. < Etot = -5389.1106 EKtot = 1273.8716 EPtot = -6662.9823 < BOND = 1.7981 ANGLE = 7.6324 DIHED = 12.0311 < 1-4 NB = 2.6256 1-4 EEL = 47.7308 VDWAALS = 999.0436 < EELEC = -7733.8439 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 90 TIME(PS) = 30.190 TEMP(K) = 300.80 PRESS = 0. < Etot = -5389.2183 EKtot = 1258.8635 EPtot = -6648.0818 < BOND = 1.6835 ANGLE = 6.9811 DIHED = 12.3073 < 1-4 NB = 3.5164 1-4 EEL = 47.3840 VDWAALS = 1010.5608 < EELEC = -7730.5150 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 100 TIME(PS) = 30.200 TEMP(K) = 294.51 PRESS = 0. < Etot = -5389.2407 EKtot = 1232.5305 EPtot = -6621.7711 < BOND = 0.5862 ANGLE = 6.6649 DIHED = 11.7161 < 1-4 NB = 3.4144 1-4 EEL = 50.4569 VDWAALS = 1019.7991 < EELEC = -7714.4088 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < A V E R A G E S O V E R 100 S T E P S < NSTEP = 100 TIME(PS) = 30.200 TEMP(K) = 302.43 PRESS = 0. < Etot = -5388.9735 EKtot = 1265.6597 EPtot = -6654.6332 < BOND = 1.9708 ANGLE = 6.6025 DIHED = 11.1770 < 1-4 NB = 3.1533 1-4 EEL = 48.3327 VDWAALS = 975.1012 < EELEC = -7700.9708 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < R M S F L U C T U A T I O N S < NSTEP = 100 TIME(PS) = 30.200 TEMP(K) = 4.95 PRESS = 0. < Etot = 0.1711 EKtot = 20.7184 EPtot = 20.7141 < BOND = 0.7958 ANGLE = 1.5576 DIHED = 0.5984 < 1-4 NB = 0.5389 1-4 EEL = 1.8777 VDWAALS = 26.3158 < EELEC = 24.1861 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --------------------------------------- possible FAILURE: check md.out.dif /home/makoto/amber12/test/nc_restart/restartMD.ntx1 1,162d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < [-O]verwriting output < File Assignments: < Here is the input file: < Ala2 explicit solvent MD using netcdf restart coords only < &cntrl < imin = 0, nstlim = 100, dt=0.001, < ntx = 1, irest = 0, ig = 1, ntxo = 1, < ntwx = 50, ioutfm = 1, ntpr = 10, ntwr = 50000, < iwrap = 0, nscm = 0, < ntc = 2, ntf = 2, ntb = 1, cut = 8.0, < ntt = 1, tautp = 5.0, temp0 = 300.0, tempi = 300.0, < ntp = 0, taup = 5.0, < &end < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting box info from netcdf restart file < NATOM = 2101 NTYPES = 9 NBONH = 2091 MBONA = 9 < NTHETH = 25 MTHETA = 11 NPHIH = 43 MPHIA = 24 < NHPARM = 0 NPARM = 0 NNB = 2871 NRES = 696 < NBONA = 9 NTHETA = 11 NPHIA = 24 NUMBND = 10 < NUMANG = 16 NPTRA = 19 NATYP = 9 NPHB = 1 < IFBOX = 2 NMXRS = 10 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < BOX TYPE: TRUNCATED OCTAHEDRON < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < ACE < General flags: < imin = 0, nmropt = 0 < Nature and format of input: < ntx = 1, irest = 0, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 10, ntrx = 1, ntwr = 50000 < iwrap = 0, ntwx = 50, ntwv = 0, ntwe = 0 < ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 1, igb = 0, nsnb = 25 < ipol = 0, gbsa = 0, iesp = 0 < dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 < Frozen or restrained atoms: < ibelly = 0, ntr = 0 < Molecular dynamics: < nstlim = 100, nscm = 0, nrespa = 1 < t = 0., dt = 0.00100, vlimit = 20.00000 < Berendsen (weak-coupling) temperature regulation: < temp0 = 300.00000, tempi = 300.00000, tautp = 5.00000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0.00001 < Ewald parameters: < verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 < vdwmeth = 1, eedmeth = 1, netfrc = 1 < Box X = 30.264 Box Y = 30.264 Box Z = 30.264 < Alpha = 109.471 Beta = 109.471 Gamma = 109.471 < NFFT1 = 30 NFFT2 = 30 NFFT3 = 30 < Cutoff= 8.000 Tol =0.100E-4 < Ewald Coefficient = 0.34864 < Interpolation order = 4 < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < ACE < begin time read from input coords = 30.100 ps < Number of triangulated 3-point waters found: 693 < Sum of charges from parm topology file = 0. < Forcing neutrality... < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < --------------------------------------------------- < APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION < using 5000.0 points per unit in tabled values < TESTING RELATIVE ERROR over r ranging from 0. to cutoff < --------------------------------------------------- < NSTEP = 0 TIME(PS) = 30.100 TEMP(K) = 457.23 PRESS = 0. < Etot = -4730.8453 EKtot = 1913.5358 EPtot = -6644.3811 < BOND = 1.2647 ANGLE = 5.2566 DIHED = 10.1909 < 1-4 NB = 3.4694 1-4 EEL = 49.4647 VDWAALS = 951.6905 < EELEC = -7665.7179 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 10 TIME(PS) = 30.110 TEMP(K) = 303.07 PRESS = 0. < Etot = -5372.1339 EKtot = 1268.3666 EPtot = -6640.5005 < BOND = 1.0066 ANGLE = 6.6477 DIHED = 11.5100 < 1-4 NB = 3.3482 1-4 EEL = 50.8322 VDWAALS = 930.9350 < EELEC = -7644.7802 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 30.120 TEMP(K) = 306.18 PRESS = 0. < Etot = -5372.2912 EKtot = 1281.3879 EPtot = -6653.6791 < BOND = 1.5486 ANGLE = 4.8080 DIHED = 10.6411 < 1-4 NB = 2.9122 1-4 EEL = 49.8069 VDWAALS = 921.2871 < EELEC = -7644.6830 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 30.130 TEMP(K) = 299.81 PRESS = 0. < Etot = -5372.2907 EKtot = 1254.7070 EPtot = -6626.9977 < BOND = 4.2838 ANGLE = 4.0291 DIHED = 10.2179 < 1-4 NB = 2.7896 1-4 EEL = 48.3830 VDWAALS = 916.4560 < EELEC = -7613.1570 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 30.140 TEMP(K) = 296.87 PRESS = 0. < Etot = -5372.3311 EKtot = 1242.3992 EPtot = -6614.7304 < BOND = 3.3849 ANGLE = 5.5955 DIHED = 10.6808 < 1-4 NB = 3.0933 1-4 EEL = 46.7371 VDWAALS = 905.5439 < EELEC = -7589.7660 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 30.150 TEMP(K) = 297.30 PRESS = 0. < Etot = -5372.2110 EKtot = 1244.2285 EPtot = -6616.4395 < BOND = 2.5217 ANGLE = 6.9334 DIHED = 10.5804 < 1-4 NB = 2.6345 1-4 EEL = 46.7280 VDWAALS = 899.3851 < EELEC = -7585.2225 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 60 TIME(PS) = 30.160 TEMP(K) = 297.17 PRESS = 0. < Etot = -5372.1749 EKtot = 1243.6627 EPtot = -6615.8376 < BOND = 2.2961 ANGLE = 7.0782 DIHED = 11.3990 < 1-4 NB = 2.4314 1-4 EEL = 47.6248 VDWAALS = 910.0249 < EELEC = -7596.6920 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 70 TIME(PS) = 30.170 TEMP(K) = 300.85 PRESS = 0. < Etot = -5372.1491 EKtot = 1259.0720 EPtot = -6631.2211 < BOND = 3.0717 ANGLE = 8.2314 DIHED = 11.3112 < 1-4 NB = 2.9997 1-4 EEL = 47.2582 VDWAALS = 930.7161 < EELEC = -7634.8095 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 80 TIME(PS) = 30.180 TEMP(K) = 299.84 PRESS = 0. < Etot = -5372.2351 EKtot = 1254.8466 EPtot = -6627.0818 < BOND = 3.7959 ANGLE = 5.6360 DIHED = 11.2860 < 1-4 NB = 2.8228 1-4 EEL = 48.6555 VDWAALS = 945.1387 < EELEC = -7644.4167 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 90 TIME(PS) = 30.190 TEMP(K) = 301.36 PRESS = 0. < Etot = -5372.1931 EKtot = 1261.1874 EPtot = -6633.3804 < BOND = 3.1356 ANGLE = 5.8024 DIHED = 11.6096 < 1-4 NB = 3.6506 1-4 EEL = 48.7888 VDWAALS = 953.3601 < EELEC = -7659.7275 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 100 TIME(PS) = 30.200 TEMP(K) = 297.39 PRESS = 0. < Etot = -5372.0880 EKtot = 1244.5904 EPtot = -6616.6784 < BOND = 1.5139 ANGLE = 6.4960 DIHED = 11.4384 < 1-4 NB = 3.2127 1-4 EEL = 48.9998 VDWAALS = 964.3594 < EELEC = -7652.6987 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < A V E R A G E S O V E R 100 S T E P S < NSTEP = 100 TIME(PS) = 30.200 TEMP(K) = 300.79 PRESS = 0. < Etot = -5370.5320 EKtot = 1258.8338 EPtot = -6629.3657 < BOND = 2.3398 ANGLE = 6.0607 DIHED = 11.0149 < 1-4 NB = 3.0021 1-4 EEL = 48.3884 VDWAALS = 926.9623 < EELEC = -7627.1339 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < R M S F L U C T U A T I O N S < NSTEP = 100 TIME(PS) = 30.200 TEMP(K) = 5.28 PRESS = 0. < Etot = 16.8559 EKtot = 22.0824 EPtot = 12.3536 < BOND = 0.8795 ANGLE = 0.9726 DIHED = 0.4930 < 1-4 NB = 0.3467 1-4 EEL = 1.3099 VDWAALS = 19.0279 < EELEC = 27.1992 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --------------------------------------- possible FAILURE: check rem.log.dif /home/makoto/amber12/test/rem_hybrid 1,24d0 < # Replica Exchange log file < # numexchg is 5 < # HYBRID REMD: < # using igb= 1 for exchange energies. < # number of closest waters kept= 50 < # REMD filenames: < # remlog= rem.log < # remtype= rem.type < # Rep#, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate (i,i+1), ResStruct# < # exchange 1 < 1 1.05 0. -615.76 300.00 330.00 0. -1 < 2 0.95 0. -615.76 330.00 300.00 2.00 -1 < # exchange 2 < 1 -1.00 306.08 -631.47 330.00 330.00 1.00 -1 < 2 -1.00 287.72 -633.87 300.00 300.00 0. -1 < # exchange 3 < 1 0.95 315.10 -637.78 330.00 300.00 1.33 -1 < 2 1.05 293.53 -645.99 300.00 330.00 0. -1 < # exchange 4 < 1 -1.00 305.10 -644.09 300.00 300.00 0. -1 < 2 -1.00 313.61 -618.81 330.00 330.00 1.00 -1 < # exchange 5 < 1 1.05 307.41 -631.69 300.00 330.00 0. -1 < 2 0.95 323.83 -629.60 330.00 300.00 1.20 -1 --------------------------------------- possible FAILURE: check rem.out.000.dif /home/makoto/amber12/test/rem_hybrid --------------------------------------- possible FAILURE: check mdout.dif /home/makoto/amber12/test/ncsu/smd 1,238d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < File Assignments: < Here is the input file: < &cntrl < igb = 0, ntx = 5, irest = 1, < ntb = 1, ntp = 0, temp0 = 300., < ntt = 3, gamma_ln = 1., < ntf = 2, ntc = 2, tol = 0.0000, < cut = 8., dt = 0.00, < ntpr = 5, ntwx = 0, nstlim = 50 < / < ncsu_smd < output_file = 'smd.txt' < output_freq = 1 < variable ! backbone RMSD w.r.t. folded state < path = (X, 5.) < harm = (0., 10., 20., 30., 40., 50., 50., 50., 50.) < type = MULTI_RMSD < # list of participating atoms < i = (1, 5, 8, 10, 12, 29, 31, 33, 41, < 43, 53, 55, 57, 59, 70, 72, 74, < 84, 86, 88, 91, 93, 95, 105, 107, < 109, 129, 131, 133, 136) < # reference coordinates < r = (-0.29, 4.03, -17.15, 0.47, 4.46, -16.54, < 1.93, 4.40, -16.85, 2.78, 4.75, -16.00, < 4.24, 4.79, -16.12, 4.93, 4.19, -14.90, < 6.13, 3.68, -15.06, 6.94, 3.05, -14.02, < 8.38, 3.58, -14.03, 8.73, 4.54, -13.17, < 10.07, 5.08, -13.08, 11.16, 4.09, -12.71, < 10.86, 2.98, -12.09, 11.82, 1.94, -11.73, < 12.35, 1.16, -12.92, 11.67, 1.15, -14.03, < 12.09, 0.51, -15.29, 12.13, 1.46, -16.47, < 11.48, 2.61, -16.39, 11.36, 3.58, -17.46, < 10.38, 3.19, -18.54, 9.30, 2.52, -18.22, < 8.35, 1.93, -19.17, 6.91, 2.35, -18.92, < 6.06, 2.25, -19.92, 4.66, 2.61, -19.91, < 3.76, 1.41, -19.92, 2.69, 1.45, -19.46, < 1.69, 0.44, -19.40, 0.61, 0.77, -18.87) < end variable < end ncsu_smd < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting new box info from bottom of inpcrd < NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 < NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 < NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 < NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 < NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 < IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < BOX TYPE: TRUNCATED OCTAHEDRON < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < NGLY < General flags: < imin = 0, nmropt = 0 < Nature and format of input: < ntx = 5, irest = 1, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 5, ntrx = 1, ntwr = 500 < iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 < ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 1, igb = 0, nsnb = 25 < ipol = 0, gbsa = 0, iesp = 0 < dielc = 1.0000, cut = 8.0000, intdiel = 1.0000 < Frozen or restrained atoms: < ibelly = 0, ntr = 0 < Molecular dynamics: < nstlim = 50, nscm = 1000, nrespa = 1 < t = 0., dt = 0.0020, vlimit = 20.0000 < Langevin dynamics temperature regulation: < ig = 71277 < temp0 = 300.0000, tempi = 0., gamma_ln= 1.0000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0.0000 < Ewald parameters: < verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 < vdwmeth = 1, eedmeth = 1, netfrc = 1 < Box X = 34.47 Box Y = 34.47 Box Z = 34.47 < Alpha = 109.47 Beta = 109.47 Gamma = 109.47 < NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 < Cutoff= 8.00 Tol =0.10E-4 < Ewald Coefficient = 0.3486 < Interpolation order = 4 < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < NGLY < begin time read from input coords = 0. ps < Number of triangulated 3-point waters found: 1001 < Sum of charges from parm topology file = -0.0000000 < Forcing neutrality... < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < NCSU : * * * * * * * * S T E E R E D M.D. * * * * * * * * * < NCSU : < NCSU : output_file = smd.txt < NCSU : output_freq = 1 (0.002 ps) < NCSU : < NCSU : CV #1 < NCSU : < NCSU : <> path = (6.231, 5.000) < NCSU : <> path_mode = SPLINE < NCSU : <> harm = (0.000, 10.000, 20.000, 30.000, < NCSU : 40.000, 50.000, 50.000, 50.000, 50.000) < NCSU : <> harm_mode = SPLINE < NCSU : < NCSU : type = 'MULTI_RMSD' < NCSU : <> group <> #1: < NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], < NCSU : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], < NCSU : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], < NCSU : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], < NCSU : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], < NCSU : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) < NCSU : reference coordinates : < NCSU : 1 : -0.29, 4.03, -17.15 < NCSU : 5 : 0.47, 4.46, -16.54 < NCSU : 8 : 1.93, 4.40, -16.85 < NCSU : 10 : 2.78, 4.75, -16.00 < NCSU : 12 : 4.24, 4.79, -16.12 < NCSU : 29 : 4.93, 4.19, -14.90 < NCSU : 31 : 6.13, 3.68, -15.06 < NCSU : 33 : 6.94, 3.05, -14.02 < NCSU : 41 : 8.38, 3.58, -14.03 < NCSU : 43 : 8.73, 4.54, -13.17 < NCSU : 53 : 10.07, 5.08, -13.08 < NCSU : 55 : 11.16, 4.09, -12.71 < NCSU : 57 : 10.86, 2.98, -12.09 < NCSU : 59 : 11.82, 1.94, -11.73 < NCSU : 70 : 12.35, 1.16, -12.92 < NCSU : 72 : 11.67, 1.15, -14.03 < NCSU : 74 : 12.09, 0.51, -15.29 < NCSU : 84 : 12.13, 1.46, -16.47 < NCSU : 86 : 11.48, 2.61, -16.39 < NCSU : 88 : 11.36, 3.58, -17.46 < NCSU : 91 : 10.38, 3.19, -18.54 < NCSU : 93 : 9.30, 2.52, -18.22 < NCSU : 95 : 8.35, 1.93, -19.17 < NCSU : 105 : 6.91, 2.35, -18.92 < NCSU : 107 : 6.06, 2.25, -19.92 < NCSU : 109 : 4.66, 2.61, -19.91 < NCSU : 129 : 3.76, 1.41, -19.92 < NCSU : 131 : 2.69, 1.45, -19.46 < NCSU : 133 : 1.69, 0.44, -19.40 < NCSU : 136 : 0.61, 0.77, -18.87 < NCSU : < NCSU : * * * * * * * * * * * * * * * * * * * * * * * * < --------------------------------------------------- < APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION < using 5000. points per unit in tabled values < TESTING RELATIVE ERROR over r ranging from 0. to cutoff < --------------------------------------------------- < NSTEP = 5 TIME(PS) = 0.01 TEMP(K) = 302.6 PRESS = 0. < Etot = -8321.484 EKtot = 1914.181 EPtot = -10235.665 < BOND = 19.073 ANGLE = 63.592 DIHED = 72.696 < 1-4 NB = 31.932 1-4 EEL = 541.000 VDWAALS = 1297.273 < EELEC = -12261.233 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 10 TIME(PS) = 0.02 TEMP(K) = 303.1 PRESS = 0. < Etot = -8329.346 EKtot = 1917.153 EPtot = -10246.499 < BOND = 25.270 ANGLE = 68.103 DIHED = 73.105 < 1-4 NB = 34.018 1-4 EEL = 541.646 VDWAALS = 1326.260 < EELEC = -12314.903 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 15 TIME(PS) = 0.03 TEMP(K) = 297.2 PRESS = 0. < Etot = -8320.093 EKtot = 1879.646 EPtot = -10199.740 < BOND = 25.714 ANGLE = 67.693 DIHED = 76.294 < 1-4 NB = 31.498 1-4 EEL = 535.070 VDWAALS = 1359.514 < EELEC = -12295.524 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 0.04 TEMP(K) = 299.1 PRESS = 0. < Etot = -8311.974 EKtot = 1891.986 EPtot = -10203.960 < BOND = 32.814 ANGLE = 68.224 DIHED = 72.902 < 1-4 NB = 28.418 1-4 EEL = 536.508 VDWAALS = 1387.057 < EELEC = -12329.884 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 25 TIME(PS) = 0.05 TEMP(K) = 301.7 PRESS = 0. < Etot = -8313.697 EKtot = 1908.548 EPtot = -10222.246 < BOND = 35.406 ANGLE = 70.794 DIHED = 73.449 < 1-4 NB = 28.956 1-4 EEL = 539.144 VDWAALS = 1406.785 < EELEC = -12376.783 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 0.06 TEMP(K) = 307.8 PRESS = 0. < Etot = -8308.410 EKtot = 1947.056 EPtot = -10255.467 < BOND = 32.447 ANGLE = 64.351 DIHED = 74.405 < 1-4 NB = 30.346 1-4 EEL = 535.080 VDWAALS = 1408.068 < EELEC = -12400.167 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 35 TIME(PS) = 0.07 TEMP(K) = 296.0 PRESS = 0. < Etot = -8312.175 EKtot = 1872.148 EPtot = -10184.323 < BOND = 23.620 ANGLE = 70.461 DIHED = 73.453 < 1-4 NB = 30.418 1-4 EEL = 532.167 VDWAALS = 1412.069 < EELEC = -12326.513 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 0.08 TEMP(K) = 300.1 PRESS = 0. < Etot = -8315.722 EKtot = 1898.261 EPtot = -10213.983 < BOND = 27.271 ANGLE = 63.010 DIHED = 74.567 < 1-4 NB = 35.060 1-4 EEL = 532.736 VDWAALS = 1410.915 < EELEC = -12357.545 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 45 TIME(PS) = 0.09 TEMP(K) = 299.0 PRESS = 0. < Etot = -8319.835 EKtot = 1891.206 EPtot = -10211.041 < BOND = 28.195 ANGLE = 58.952 DIHED = 74.489 < 1-4 NB = 36.331 1-4 EEL = 535.683 VDWAALS = 1407.683 < EELEC = -12352.377 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 305.2 PRESS = 0. < Etot = -8321.773 EKtot = 1930.709 EPtot = -10252.483 < BOND = 22.445 ANGLE = 69.872 DIHED = 71.349 < 1-4 NB = 36.237 1-4 EEL = 538.154 VDWAALS = 1393.610 < EELEC = -12384.152 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < A V E R A G E S O V E R 50 S T E P S < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 300.6 PRESS = 0. < Etot = -8317.155 EKtot = 1901.420 EPtot = -10218.575 < BOND = 28.736 ANGLE = 67.445 DIHED = 73.769 < 1-4 NB = 32.212 1-4 EEL = 536.834 VDWAALS = 1376.174 < EELEC = -12333.749 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < R M S F L U C T U A T I O N S < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 3.2 PRESS = 0. < Etot = 6.819 EKtot = 20.478 EPtot = 20.568 < BOND = 4.595 ANGLE = 4.127 DIHED = 1.957 < 1-4 NB = 2.612 1-4 EEL = 3.259 VDWAALS = 43.525 < EELEC = 42.433 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --------------------------------------- possible FAILURE: check smd.txt.dif /home/makoto/amber12/test/ncsu/smd 1,56d0 < # < # MD time (ps), CV, handle_position, spring_constant, work < # < 0. 6.2315682 6.2315682 0. 0. < 0.002 6.2348041 6.2301100 0.4710400 0.0000068 < 0.004 6.2380460 6.2258143 1.7203200 0.0001502 < 0.006 6.2414006 6.2187993 3.5020800 0.0009567 < 0.008 6.2447542 6.2091832 5.5705600 0.0035986 < 0.010 6.2482556 6.1970843 7.6800000 0.0099365 < 0.012 6.2517789 6.1826207 9.5846400 0.0221270 < 0.014 6.2552896 6.1659108 11.2000000 0.0424810 < 0.016 6.2585766 6.1470727 12.8000000 0.0752996 < 0.018 6.2614603 6.1262247 14.4000000 0.1251078 < 0.020 6.2635324 6.1034851 16.0000000 0.1968568 < 0.022 6.2647066 6.0789719 17.6000000 0.2959066 < 0.024 6.2649343 6.0528036 19.2000000 0.4279681 < 0.026 6.2643008 6.0250982 20.8000000 0.5990860 < 0.028 6.2633488 5.9959741 22.4000000 0.8159447 < 0.030 6.2625146 5.9655494 24.0000000 1.0860257 < 0.032 6.2619672 5.9339425 25.6000000 1.4174487 < 0.034 6.2619709 5.9012714 27.2000000 1.8189766 < 0.036 6.2623477 5.8676545 28.8000000 2.2995752 < 0.038 6.2627737 5.8332100 30.4000000 2.8678641 < 0.040 6.2633554 5.7980562 32.0000000 3.5323127 < 0.042 6.2640303 5.7623111 33.6000000 4.3010953 < 0.044 6.2649040 5.7260932 35.2000000 5.1820834 < 0.046 6.2660473 5.6895205 36.8000000 6.1827769 < 0.048 6.2673634 5.6527114 38.4000000 7.3098850 < 0.050 6.2689229 5.6157841 40.0000000 8.5693221 < 0.052 6.2704476 5.5788567 41.7075200 9.9926235 < 0.054 6.2719883 5.5420476 43.5481600 11.5988894 < 0.056 6.2731156 5.5054750 45.3990400 13.3627845 < 0.058 6.2736219 5.4692570 47.1372800 15.2428206 < 0.060 6.2733562 5.4335120 48.6400000 17.1805232 < 0.062 6.2723088 5.3983581 49.7843200 19.1003075 < 0.064 6.2706654 5.3639136 50.4646400 20.9173815 < 0.066 6.2685679 5.3302967 50.7257600 22.6014462 < 0.068 6.2663943 5.2976257 50.6899200 24.1642946 < 0.070 6.2641845 5.2660187 50.4800000 25.6320744 < 0.072 6.2622712 5.2355940 50.2188800 27.0452917 < 0.074 6.2607601 5.2064699 50.0294400 28.4588910 < 0.076 6.2593363 5.1787645 50.0000000 29.9208112 < 0.078 6.2581160 5.1525962 50.0000000 31.3509721 < 0.080 6.2570812 5.1280830 50.0000000 32.7203480 < 0.082 6.2559396 5.1053434 50.0000000 34.0162789 < 0.084 6.2544557 5.0844954 50.0000000 35.2257522 < 0.086 6.2525421 5.0656573 50.0000000 36.3357124 < 0.088 6.2502700 5.0489474 50.0000000 37.3333811 < 0.090 6.2474976 5.0344839 50.0000000 38.2063771 < 0.092 6.2443438 5.0223849 50.0000000 38.9428910 < 0.094 6.2408099 5.0127689 50.0000000 39.5318761 < 0.096 6.2372871 5.0057538 50.0000000 39.9632248 < 0.098 6.2339445 5.0014581 50.0000000 40.2278426 < # < # <> total work done: 40.227842642 < # --------------------------------------- possible FAILURE: check mdout.dif /home/makoto/amber12/test/ncsu/pmd 1,231d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < File Assignments: < Here is the input file: < &cntrl < igb = 0, ntx = 5, irest = 1, < ntb = 1, ntp = 0, temp0 = 300., < ntt = 3, gamma_ln = 1., < ntf = 2, ntc = 2, tol = 0.0000, < cut = 8., dt = 0.00, < ntpr = 5, ntwx = 0, nstlim = 50 < / < ncsu_pmd < output_file = 'pmd.txt' < output_freq = 1 < variable ! backbone RMSD w.r.t. folded state < anchor_position = 6. < anchor_strength = 10. < type = MULTI_RMSD < # list of participating atoms < i = (1, 5, 8, 10, 12, 29, 31, 33, 41, < 43, 53, 55, 57, 59, 70, 72, 74, < 84, 86, 88, 91, 93, 95, 105, 107, < 109, 129, 131, 133, 136) < # reference coordinates < r = (-0.29, 4.03, -17.15, 0.47, 4.46, -16.54, < 1.93, 4.40, -16.85, 2.78, 4.75, -16.00, < 4.24, 4.79, -16.12, 4.93, 4.19, -14.90, < 6.13, 3.68, -15.06, 6.94, 3.05, -14.02, < 8.38, 3.58, -14.03, 8.73, 4.54, -13.17, < 10.07, 5.08, -13.08, 11.16, 4.09, -12.71, < 10.86, 2.98, -12.09, 11.82, 1.94, -11.73, < 12.35, 1.16, -12.92, 11.67, 1.15, -14.03, < 12.09, 0.51, -15.29, 12.13, 1.46, -16.47, < 11.48, 2.61, -16.39, 11.36, 3.58, -17.46, < 10.38, 3.19, -18.54, 9.30, 2.52, -18.22, < 8.35, 1.93, -19.17, 6.91, 2.35, -18.92, < 6.06, 2.25, -19.92, 4.66, 2.61, -19.91, < 3.76, 1.41, -19.92, 2.69, 1.45, -19.46, < 1.69, 0.44, -19.40, 0.61, 0.77, -18.87) < end variable < end ncsu_pmd < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting new box info from bottom of inpcrd < NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 < NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 < NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 < NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 < NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 < IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < BOX TYPE: TRUNCATED OCTAHEDRON < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < NGLY < General flags: < imin = 0, nmropt = 0 < Nature and format of input: < ntx = 5, irest = 1, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 5, ntrx = 1, ntwr = 500 < iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 < ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 1, igb = 0, nsnb = 25 < ipol = 0, gbsa = 0, iesp = 0 < dielc = 1.0000, cut = 8.0000, intdiel = 1.0000 < Frozen or restrained atoms: < ibelly = 0, ntr = 0 < Molecular dynamics: < nstlim = 50, nscm = 1000, nrespa = 1 < t = 0., dt = 0.0020, vlimit = 20.0000 < Langevin dynamics temperature regulation: < ig = 71277 < temp0 = 300.0000, tempi = 0., gamma_ln= 1.0000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0.0000 < Ewald parameters: < verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 < vdwmeth = 1, eedmeth = 1, netfrc = 1 < Box X = 34.47 Box Y = 34.47 Box Z = 34.47 < Alpha = 109.47 Beta = 109.47 Gamma = 109.47 < NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 < Cutoff= 8.00 Tol =0.10E-4 < Ewald Coefficient = 0.3486 < Interpolation order = 4 < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < NGLY < begin time read from input coords = 0. ps < Number of triangulated 3-point waters found: 1001 < Sum of charges from parm topology file = -0.0000000 < Forcing neutrality... < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < NCSU : < NCSU : output_file = pmd.txt < NCSU : output_freq = 1 (0.002 ps) < NCSU : < NCSU : CV #1 << anchor : position = 6.00000, strength = 10.00000 >> < NCSU : type = 'MULTI_RMSD' < NCSU : <> group <> #1: < NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], < NCSU : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], < NCSU : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], < NCSU : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], < NCSU : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], < NCSU : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) < NCSU : reference coordinates : < NCSU : 1 : -0.29, 4.03, -17.15 < NCSU : 5 : 0.47, 4.46, -16.54 < NCSU : 8 : 1.93, 4.40, -16.85 < NCSU : 10 : 2.78, 4.75, -16.00 < NCSU : 12 : 4.24, 4.79, -16.12 < NCSU : 29 : 4.93, 4.19, -14.90 < NCSU : 31 : 6.13, 3.68, -15.06 < NCSU : 33 : 6.94, 3.05, -14.02 < NCSU : 41 : 8.38, 3.58, -14.03 < NCSU : 43 : 8.73, 4.54, -13.17 < NCSU : 53 : 10.07, 5.08, -13.08 < NCSU : 55 : 11.16, 4.09, -12.71 < NCSU : 57 : 10.86, 2.98, -12.09 < NCSU : 59 : 11.82, 1.94, -11.73 < NCSU : 70 : 12.35, 1.16, -12.92 < NCSU : 72 : 11.67, 1.15, -14.03 < NCSU : 74 : 12.09, 0.51, -15.29 < NCSU : 84 : 12.13, 1.46, -16.47 < NCSU : 86 : 11.48, 2.61, -16.39 < NCSU : 88 : 11.36, 3.58, -17.46 < NCSU : 91 : 10.38, 3.19, -18.54 < NCSU : 93 : 9.30, 2.52, -18.22 < NCSU : 95 : 8.35, 1.93, -19.17 < NCSU : 105 : 6.91, 2.35, -18.92 < NCSU : 107 : 6.06, 2.25, -19.92 < NCSU : 109 : 4.66, 2.61, -19.91 < NCSU : 129 : 3.76, 1.41, -19.92 < NCSU : 131 : 2.69, 1.45, -19.46 < NCSU : 133 : 1.69, 0.44, -19.40 < NCSU : 136 : 0.61, 0.77, -18.87 < NCSU : < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < --------------------------------------------------- < APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION < using 5000. points per unit in tabled values < TESTING RELATIVE ERROR over r ranging from 0. to cutoff < --------------------------------------------------- < NSTEP = 5 TIME(PS) = 0.01 TEMP(K) = 302.6 PRESS = 0. < Etot = -8321.518 EKtot = 1914.146 EPtot = -10235.665 < BOND = 19.066 ANGLE = 63.597 DIHED = 72.694 < 1-4 NB = 31.933 1-4 EEL = 541.008 VDWAALS = 1297.272 < EELEC = -12261.238 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 10 TIME(PS) = 0.02 TEMP(K) = 303.1 PRESS = 0. < Etot = -8329.410 EKtot = 1917.121 EPtot = -10246.532 < BOND = 25.239 ANGLE = 68.081 DIHED = 73.111 < 1-4 NB = 34.021 1-4 EEL = 541.682 VDWAALS = 1326.258 < EELEC = -12314.926 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 15 TIME(PS) = 0.03 TEMP(K) = 297.2 PRESS = 0. < Etot = -8320.163 EKtot = 1879.592 EPtot = -10199.756 < BOND = 25.701 ANGLE = 67.655 DIHED = 76.300 < 1-4 NB = 31.510 1-4 EEL = 535.120 VDWAALS = 1359.512 < EELEC = -12295.558 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 0.04 TEMP(K) = 299.1 PRESS = 0. < Etot = -8312.045 EKtot = 1891.970 EPtot = -10204.016 < BOND = 32.790 ANGLE = 68.190 DIHED = 72.905 < 1-4 NB = 28.426 1-4 EEL = 536.529 VDWAALS = 1387.049 < EELEC = -12329.907 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 25 TIME(PS) = 0.05 TEMP(K) = 301.7 PRESS = 0. < Etot = -8313.699 EKtot = 1908.613 EPtot = -10222.312 < BOND = 35.390 ANGLE = 70.794 DIHED = 73.473 < 1-4 NB = 28.933 1-4 EEL = 539.046 VDWAALS = 1406.802 < EELEC = -12376.752 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 0.06 TEMP(K) = 307.8 PRESS = 0. < Etot = -8308.264 EKtot = 1947.081 EPtot = -10255.345 < BOND = 32.769 ANGLE = 64.371 DIHED = 74.423 < 1-4 NB = 30.255 1-4 EEL = 534.720 VDWAALS = 1408.105 < EELEC = -12399.991 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 35 TIME(PS) = 0.07 TEMP(K) = 295.9 PRESS = 0. < Etot = -8312.460 EKtot = 1871.922 EPtot = -10184.382 < BOND = 23.704 ANGLE = 70.796 DIHED = 73.511 < 1-4 NB = 30.205 1-4 EEL = 531.380 VDWAALS = 1412.158 < EELEC = -12326.138 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 0.08 TEMP(K) = 300.0 PRESS = 0. < Etot = -8316.436 EKtot = 1897.677 EPtot = -10214.113 < BOND = 27.547 ANGLE = 63.410 DIHED = 74.681 < 1-4 NB = 34.627 1-4 EEL = 531.296 VDWAALS = 1411.070 < EELEC = -12356.748 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 45 TIME(PS) = 0.09 TEMP(K) = 298.9 PRESS = 0. < Etot = -8320.814 EKtot = 1890.491 EPtot = -10211.305 < BOND = 28.980 ANGLE = 59.062 DIHED = 74.581 < 1-4 NB = 35.651 1-4 EEL = 533.488 VDWAALS = 1407.950 < EELEC = -12351.019 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 305.2 PRESS = 0. < Etot = -8323.558 EKtot = 1930.495 EPtot = -10254.053 < BOND = 22.605 ANGLE = 69.799 DIHED = 71.611 < 1-4 NB = 35.212 1-4 EEL = 535.279 VDWAALS = 1393.425 < EELEC = -12381.986 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < A V E R A G E S O V E R 50 S T E P S < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 300.6 PRESS = 0. < Etot = -8317.459 EKtot = 1901.250 EPtot = -10218.709 < BOND = 28.897 ANGLE = 67.515 DIHED = 73.817 < 1-4 NB = 32.014 1-4 EEL = 536.190 VDWAALS = 1376.216 < EELEC = -12333.361 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < R M S F L U C T U A T I O N S < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 3.2 PRESS = 0. < Etot = 6.879 EKtot = 20.551 EPtot = 20.601 < BOND = 4.599 ANGLE = 4.105 DIHED = 1.952 < 1-4 NB = 2.411 1-4 EEL = 3.676 VDWAALS = 43.564 < EELEC = 42.185 EHBOND = 0. RESTRAINT = 0. < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --------------------------------------- possible FAILURE: check pmd.txt.dif /home/makoto/amber12/test/ncsu/pmd 1,55d0 < # = NCSU%PMD ================================================================== < # << anchor(1) : position = 6.00000, strength = 10.00000 >> < # ----------------------------------------------------------------------------- < # MD time (ps), CV(1:1) < # ============================================================================= < 0. 6.2315682 < 0.002 6.2347940 < 0.004 6.2380163 < 0.006 6.2413428 < 0.008 6.2446613 < 0.010 6.2481220 < 0.012 6.2516006 < 0.014 6.2550639 < 0.016 6.2583022 < 0.018 6.2611371 < 0.020 6.2631620 < 0.022 6.2642928 < 0.024 6.2644832 < 0.026 6.2638217 < 0.028 6.2628538 < 0.030 6.2620193 < 0.032 6.2614905 < 0.034 6.2615353 < 0.036 6.2619796 < 0.038 6.2625035 < 0.040 6.2632176 < 0.042 6.2640639 < 0.044 6.2651523 < 0.046 6.2665584 < 0.048 6.2681902 < 0.050 6.2701233 < 0.052 6.2720848 < 0.054 6.2741316 < 0.056 6.2758406 < 0.058 6.2770110 < 0.060 6.2774978 < 0.062 6.2772963 < 0.064 6.2765949 < 0.066 6.2755364 < 0.068 6.2744975 < 0.070 6.2735161 < 0.072 6.2729217 < 0.074 6.2728166 < 0.076 6.2728828 < 0.078 6.2732327 < 0.080 6.2738428 < 0.082 6.2744153 < 0.084 6.2747092 < 0.086 6.2746341 < 0.088 6.2742629 < 0.090 6.2734620 < 0.092 6.2723595 < 0.094 6.2709609 < 0.096 6.2696511 < 0.098 6.2685841 --------------------------------------- possible FAILURE: check mdout.dif /home/makoto/amber12/test/ncsu/smd2 1,191d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < File Assignments: < Here is the input file: < &cntrl < cut = 77., ntb = 0, ntp = 0, ntt = 3, gamma_ln = 1., < irest = 1, ntx = 5, ntc = 2, ntf = 2, tol = 0.00000, < ioutfm = 1, igb = 2, gbsa = 1, < dt = 0.00, ntpr = 50, ntwx = 0, ntwr = 500, nstlim = 500, < ig = 29166, ntr = 0, nscm = 5000 < / < ncsu_smd < ! < ! try it with path = (-5., 5.), ntwx > 0 and ntslim >= 50000 < ! < output_file = 'work.txt' < output_freq = 1 < variable < type = COS_OF_DIHEDRAL ! sum of cosines of dihedral angles < i = ( 2, 5, 7, 17, < 17, 19, 21, 31, < 31, 33, 35, 45, < 45, 47, 49, 59, < 59, 61, 63, 73) < path_mode = LINES ! steer along line segments < path = (-5., -4., -4., -5.) < harm = (100.) < harm_mode = SPLINE ! default < end variable < end ncsu_smd < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < NATOM = 82 NTYPES = 7 NBONH = 42 MBONA = 44 < NTHETH = 104 MTHETA = 64 NPHIH = 182 MPHIA = 188 < NHPARM = 0 NPARM = 0 NNB = 491 NRES = 7 < NBONA = 44 NTHETA = 64 NPHIA = 188 NUMBND = 8 < NUMANG = 18 NPTRA = 25 NATYP = 7 NPHB = 0 < IFBOX = 0 NMXRS = 14 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < ACE < General flags: < imin = 0, nmropt = 0 < Nature and format of input: < ntx = 5, irest = 1, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500 < iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 < ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 0, igb = 2, nsnb = 25 < ipol = 0, gbsa = 1, iesp = 0 < dielc = 1.0000, cut = 77.0000, intdiel = 1.0000 < saltcon = 0., offset = 0.0900, gbalpha= 0.8000 < gbbeta = 0., gbgamma = 2.9091, surften = 0.0050 < rdt = 0., rgbmax = 25.0000 extdiel = 78.5000 < alpb = 0 < Frozen or restrained atoms: < ibelly = 0, ntr = 0 < Molecular dynamics: < nstlim = 500, nscm = 5000, nrespa = 1 < t = 0., dt = 0.0020, vlimit = 20.0000 < Langevin dynamics temperature regulation: < ig = 29166 < temp0 = 300.0000, tempi = 0., gamma_ln= 1.0000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0. < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < ACE < begin time read from input coords = 0. ps < Number of triangulated 3-point waters found: 0 < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < NCSU : * * * * * * * * S T E E R E D M.D. * * * * * * * * * < NCSU : < NCSU : output_file = work.txt < NCSU : output_freq = 1 (0.002 ps) < NCSU : < NCSU : CV #1 < NCSU : < NCSU : <> path = (-5.000, -4.000, -4.000, -5.000) < NCSU : <> path_mode = LINES < NCSU : <> harm = (100.000) < NCSU : <> harm_mode = SPLINE < NCSU : < NCSU : type = 'COS_OF_DIHEDRAL' < NCSU : 2 [CH3] ==> 5 [C] ==> 7 [N] ==> 17 [CA] < NCSU : 17 [CA] ==> 19 [C] ==> 21 [N] ==> 31 [CA] < NCSU : 31 [CA] ==> 33 [C] ==> 35 [N] ==> 45 [CA] < NCSU : 45 [CA] ==> 47 [C] ==> 49 [N] ==> 59 [CA] < NCSU : 59 [CA] ==> 61 [C] ==> 63 [N] ==> 73 [CA] < NCSU : < NCSU : * * * * * * * * * * * * * * * * * * * * * * * * < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 275.9 PRESS = 0. < Etot = 167.498 EKtot = 55.931 EPtot = 111.566 < BOND = 15.856 ANGLE = 52.262 DIHED = 86.866 < 1-4 NB = 16.204 1-4 EEL = 287.957 VDWAALS = -10.942 < EELEC = -291.170 EGB = -49.056 RESTRAINT = 0. < ESURF= 3.587 < ------------------------------------------------------------------------------ < NSTEP = 100 TIME(PS) = 0.20 TEMP(K) = 288.4 PRESS = 0. < Etot = 170.703 EKtot = 58.466 EPtot = 112.237 < BOND = 14.479 ANGLE = 60.040 DIHED = 85.796 < 1-4 NB = 14.142 1-4 EEL = 282.783 VDWAALS = -11.363 < EELEC = -290.034 EGB = -47.146 RESTRAINT = 0. < ESURF= 3.538 < ------------------------------------------------------------------------------ < NSTEP = 150 TIME(PS) = 0.30 TEMP(K) = 289.6 PRESS = 0. < Etot = 177.409 EKtot = 58.700 EPtot = 118.709 < BOND = 13.954 ANGLE = 52.996 DIHED = 105.015 < 1-4 NB = 12.674 1-4 EEL = 282.421 VDWAALS = -15.502 < EELEC = -290.691 EGB = -45.679 RESTRAINT = 0. < ESURF= 3.520 < ------------------------------------------------------------------------------ < NSTEP = 200 TIME(PS) = 0.40 TEMP(K) = 302.8 PRESS = 0. < Etot = 180.930 EKtot = 61.392 EPtot = 119.537 < BOND = 16.571 ANGLE = 47.313 DIHED = 107.480 < 1-4 NB = 14.898 1-4 EEL = 286.369 VDWAALS = -16.985 < EELEC = -293.655 EGB = -45.948 RESTRAINT = 0. < ESURF= 3.492 < ------------------------------------------------------------------------------ < NSTEP = 250 TIME(PS) = 0.50 TEMP(K) = 260.8 PRESS = 0. < Etot = 187.155 EKtot = 52.878 EPtot = 134.277 < BOND = 17.106 ANGLE = 62.240 DIHED = 104.764 < 1-4 NB = 15.097 1-4 EEL = 289.554 VDWAALS = -16.770 < EELEC = -297.155 EGB = -44.072 RESTRAINT = 0. < ESURF= 3.511 < ------------------------------------------------------------------------------ < NSTEP = 300 TIME(PS) = 0.60 TEMP(K) = 282.2 PRESS = 0. < Etot = 184.470 EKtot = 57.203 EPtot = 127.267 < BOND = 17.274 ANGLE = 55.576 DIHED = 107.242 < 1-4 NB = 12.291 1-4 EEL = 286.031 VDWAALS = -15.517 < EELEC = -294.772 EGB = -44.363 RESTRAINT = 0. < ESURF= 3.504 < ------------------------------------------------------------------------------ < NSTEP = 350 TIME(PS) = 0.70 TEMP(K) = 330.8 PRESS = 0. < Etot = 182.398 EKtot = 67.051 EPtot = 115.347 < BOND = 12.971 ANGLE = 51.792 DIHED = 101.159 < 1-4 NB = 13.200 1-4 EEL = 285.457 VDWAALS = -15.741 < EELEC = -293.399 EGB = -43.655 RESTRAINT = 0. < ESURF= 3.562 < ------------------------------------------------------------------------------ < NSTEP = 400 TIME(PS) = 0.80 TEMP(K) = 306.1 PRESS = 0. < Etot = 179.599 EKtot = 62.049 EPtot = 117.549 < BOND = 17.318 ANGLE = 50.092 DIHED = 100.902 < 1-4 NB = 14.356 1-4 EEL = 283.526 VDWAALS = -14.944 < EELEC = -294.697 EGB = -42.557 RESTRAINT = 0. < ESURF= 3.552 < ------------------------------------------------------------------------------ < NSTEP = 450 TIME(PS) = 0.90 TEMP(K) = 278.2 PRESS = 0. < Etot = 170.908 EKtot = 56.406 EPtot = 114.502 < BOND = 19.960 ANGLE = 61.731 DIHED = 83.146 < 1-4 NB = 12.867 1-4 EEL = 281.114 VDWAALS = -13.570 < EELEC = -291.449 EGB = -42.884 RESTRAINT = 0. < ESURF= 3.587 < ------------------------------------------------------------------------------ < NSTEP = 500 TIME(PS) = 1.00 TEMP(K) = 274.1 PRESS = 0. < Etot = 170.052 EKtot = 55.565 EPtot = 114.486 < BOND = 9.989 ANGLE = 60.643 DIHED = 86.979 < 1-4 NB = 17.499 1-4 EEL = 282.768 VDWAALS = -11.759 < EELEC = -292.414 EGB = -42.808 RESTRAINT = 0. < ESURF= 3.588 < ------------------------------------------------------------------------------ < A V E R A G E S O V E R 500 S T E P S < NSTEP = 500 TIME(PS) = 1.00 TEMP(K) = 292.9 PRESS = 0. < Etot = 177.055 EKtot = 59.379 EPtot = 117.676 < BOND = 15.050 ANGLE = 55.562 DIHED = 96.278 < 1-4 NB = 14.242 1-4 EEL = 285.024 VDWAALS = -14.178 < EELEC = -292.969 EGB = -44.879 RESTRAINT = 0. < ESURF= 3.544 < ------------------------------------------------------------------------------ < R M S F L U C T U A T I O N S < NSTEP = 500 TIME(PS) = 1.00 TEMP(K) = 22.1 PRESS = 0. < Etot = 7.022 EKtot = 4.487 EPtot = 8.281 < BOND = 3.063 ANGLE = 4.489 DIHED = 9.196 < 1-4 NB = 1.321 1-4 EEL = 2.071 VDWAALS = 1.785 < EELEC = 2.353 EGB = 2.154 RESTRAINT = 0. < ESURF= 0.037 < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --------------------------------------- possible FAILURE: check work.txt.dif /home/makoto/amber12/test/ncsu/smd2 1,506d0 < # < # MD time (ps), CV, handle_position, spring_constant, work < # < 0. -4.9587001 -5.0000000 100.0000000 0. < 0.002 -4.9610631 -4.9940000 100.0000000 -0.0222710 < 0.004 -4.9646120 -4.9880000 100.0000000 -0.0391684 < 0.006 -4.9676187 -4.9820000 100.0000000 -0.0504992 < 0.008 -4.9691569 -4.9760000 100.0000000 -0.0568665 < 0.010 -4.9682595 -4.9700000 100.0000000 -0.0594416 < 0.012 -4.9654447 -4.9640000 100.0000000 -0.0595303 < 0.014 -4.9615480 -4.9580000 100.0000000 -0.0580324 < 0.016 -4.9582880 -4.9520000 100.0000000 -0.0550816 < 0.018 -4.9561859 -4.9460000 100.0000000 -0.0501394 < 0.020 -4.9553622 -4.9400000 100.0000000 -0.0424749 < 0.022 -4.9554082 -4.9340000 100.0000000 -0.0314438 < 0.024 -4.9553536 -4.9280000 100.0000000 -0.0168152 < 0.026 -4.9542937 -4.9220000 100.0000000 0.0010789 < 0.028 -4.9519929 -4.9160000 100.0000000 0.0215649 < 0.030 -4.9476029 -4.9100000 100.0000000 0.0436436 < 0.032 -4.9408643 -4.9040000 100.0000000 0.0659838 < 0.034 -4.9326820 -4.8980000 100.0000000 0.0874477 < 0.036 -4.9225839 -4.8920000 100.0000000 0.1070276 < 0.038 -4.9121661 -4.8860000 100.0000000 0.1240526 < 0.040 -4.9034125 -4.8800000 100.0000000 0.1389262 < 0.042 -4.8968004 -4.8740000 100.0000000 0.1527901 < 0.044 -4.8930715 -4.8680000 100.0000000 0.1671517 < 0.046 -4.8905289 -4.8620000 100.0000000 0.1832319 < 0.048 -4.8868159 -4.8560000 100.0000000 0.2010353 < 0.050 -4.8830582 -4.8500000 100.0000000 0.2201976 < 0.052 -4.8795381 -4.8440000 100.0000000 0.2407765 < 0.054 -4.8779373 -4.8380000 100.0000000 0.2634192 < 0.056 -4.8785853 -4.8320000 100.0000000 0.2893760 < 0.058 -4.8803401 -4.8260000 100.0000000 0.3196536 < 0.060 -4.8830772 -4.8200000 100.0000000 0.3548788 < 0.062 -4.8856901 -4.8140000 100.0000000 0.3953090 < 0.064 -4.8876116 -4.8080000 100.0000000 0.4406995 < 0.066 -4.8883310 -4.8020000 100.0000000 0.4904823 < 0.068 -4.8864751 -4.7960000 100.0000000 0.5435242 < 0.070 -4.8819953 -4.7900000 100.0000000 0.5982653 < 0.072 -4.8760918 -4.7840000 100.0000000 0.6534915 < 0.074 -4.8716335 -4.7780000 100.0000000 0.7092091 < 0.076 -4.8700311 -4.7720000 100.0000000 0.7667085 < 0.078 -4.8724205 -4.7660000 100.0000000 0.8280440 < 0.080 -4.8788636 -4.7600000 100.0000000 0.8956292 < 0.082 -4.8875795 -4.7540000 100.0000000 0.9713622 < 0.084 -4.8963951 -4.7480000 100.0000000 1.0559546 < 0.086 -4.9035732 -4.7420000 100.0000000 1.1489451 < 0.088 -4.9072887 -4.7360000 100.0000000 1.2488037 < 0.090 -4.9071814 -4.7300000 100.0000000 1.3533447 < 0.092 -4.9034813 -4.7240000 100.0000000 1.4603436 < 0.094 -4.8974430 -4.7180000 100.0000000 1.5680209 < 0.096 -4.8912443 -4.7120000 100.0000000 1.6756271 < 0.098 -4.8881438 -4.7060000 100.0000000 1.7840436 < 0.100 -4.8887076 -4.7000000 100.0000000 1.8952990 < 0.102 -4.8926423 -4.6940000 100.0000000 2.0115040 < 0.104 -4.8990293 -4.6880000 100.0000000 2.1344056 < 0.106 -4.9059491 -4.6820000 100.0000000 2.2648991 < 0.108 -4.9119833 -4.6760000 100.0000000 2.4028789 < 0.110 -4.9164061 -4.6700000 100.0000000 2.5475957 < 0.112 -4.9183957 -4.6640000 100.0000000 2.6978363 < 0.114 -4.9188440 -4.6580000 100.0000000 2.8524082 < 0.116 -4.9179537 -4.6520000 100.0000000 3.0104476 < 0.118 -4.9158150 -4.6460000 100.0000000 3.1711782 < 0.120 -4.9122297 -4.6400000 100.0000000 3.3337916 < 0.122 -4.9070947 -4.6340000 100.0000000 3.4973890 < 0.124 -4.8995256 -4.6280000 100.0000000 3.6607751 < 0.126 -4.8882734 -4.6220000 100.0000000 3.8221148 < 0.128 -4.8741446 -4.6160000 100.0000000 3.9794403 < 0.130 -4.8592075 -4.6100000 100.0000000 4.1316459 < 0.132 -4.8454868 -4.6040000 100.0000000 4.2788542 < 0.134 -4.8352671 -4.5980000 100.0000000 4.4224804 < 0.136 -4.8307496 -4.5920000 100.0000000 4.5652855 < 0.138 -4.8311279 -4.5860000 100.0000000 4.7104488 < 0.140 -4.8357430 -4.5800000 100.0000000 4.8607101 < 0.142 -4.8424355 -4.5740000 100.0000000 5.0179637 < 0.144 -4.8496386 -4.5680000 100.0000000 5.1829859 < 0.146 -4.8569253 -4.5620000 100.0000000 5.3559552 < 0.148 -4.8628388 -4.5560000 100.0000000 5.5364844 < 0.150 -4.8673810 -4.5500000 100.0000000 5.7237504 < 0.152 -4.8711834 -4.5440000 100.0000000 5.9171197 < 0.154 -4.8746624 -4.5380000 100.0000000 6.1162735 < 0.156 -4.8772646 -4.5320000 100.0000000 6.3208516 < 0.158 -4.8783951 -4.5260000 100.0000000 6.5301495 < 0.160 -4.8781415 -4.5200000 100.0000000 6.7433105 < 0.162 -4.8750872 -4.5140000 100.0000000 6.9590792 < 0.164 -4.8675686 -4.5080000 100.0000000 7.1752759 < 0.166 -4.8549328 -4.5020000 100.0000000 7.3890264 < 0.168 -4.8358072 -4.4960000 100.0000000 7.5968484 < 0.170 -4.8096382 -4.4900000 100.0000000 7.7946820 < 0.172 -4.7792312 -4.4840000 100.0000000 7.9791429 < 0.174 -4.7477097 -4.4780000 100.0000000 8.1486251 < 0.176 -4.7192591 -4.4720000 100.0000000 8.3037158 < 0.178 -4.7012643 -4.4660000 100.0000000 8.4484728 < 0.180 -4.6960632 -4.4600000 100.0000000 8.5898711 < 0.182 -4.7020397 -4.4540000 100.0000000 8.7351020 < 0.184 -4.7144543 -4.4480000 100.0000000 8.8894502 < 0.186 -4.7274335 -4.4420000 100.0000000 9.0550166 < 0.188 -4.7371165 -4.4360000 100.0000000 9.2309816 < 0.190 -4.7418089 -4.4300000 100.0000000 9.4148593 < 0.192 -4.7410359 -4.4240000 100.0000000 9.6035127 < 0.194 -4.7350335 -4.4180000 100.0000000 9.7937336 < 0.196 -4.7257637 -4.4120000 100.0000000 9.9829727 < 0.198 -4.7153829 -4.4060000 100.0000000 10.1699167 < 0.200 -4.7047738 -4.4000000 100.0000000 10.3541638 < 0.202 -4.6944498 -4.3940000 100.0000000 10.5357309 < 0.204 -4.6856789 -4.3880000 100.0000000 10.7151695 < 0.206 -4.6758400 -4.3820000 100.0000000 10.8926252 < 0.208 -4.6632392 -4.3760000 100.0000000 11.0669490 < 0.210 -4.6482722 -4.3700000 100.0000000 11.2366025 < 0.212 -4.6333452 -4.3640000 100.0000000 11.4008877 < 0.214 -4.6201912 -4.3580000 100.0000000 11.5603487 < 0.216 -4.6085894 -4.3520000 100.0000000 11.7159829 < 0.218 -4.5988107 -4.3460000 100.0000000 11.8688029 < 0.220 -4.5909266 -4.3400000 100.0000000 12.0199241 < 0.222 -4.5833252 -4.3340000 100.0000000 12.1699997 < 0.224 -4.5777036 -4.3280000 100.0000000 12.3197083 < 0.226 -4.5737472 -4.3220000 100.0000000 12.4701436 < 0.228 -4.5705178 -4.3160000 100.0000000 12.6220232 < 0.230 -4.5629164 -4.3100000 100.0000000 12.7742534 < 0.232 -4.5494957 -4.3040000 100.0000000 12.9237771 < 0.234 -4.5312638 -4.2980000 100.0000000 13.0674050 < 0.236 -4.5115404 -4.2920000 100.0000000 13.2032462 < 0.238 -4.4917518 -4.2860000 100.0000000 13.3308339 < 0.240 -4.4729953 -4.2800000 100.0000000 13.4504581 < 0.242 -4.4585734 -4.2740000 100.0000000 13.5637287 < 0.244 -4.4465106 -4.2680000 100.0000000 13.6726540 < 0.246 -4.4370977 -4.2620000 100.0000000 13.7787365 < 0.248 -4.4306963 -4.2560000 100.0000000 13.8836747 < 0.250 -4.4284299 -4.2500000 100.0000000 13.9896126 < 0.252 -4.4289659 -4.2440000 100.0000000 14.0986313 < 0.254 -4.4343983 -4.2380000 100.0000000 14.2130406 < 0.256 -4.4415457 -4.2320000 100.0000000 14.3348238 < 0.258 -4.4492697 -4.2260000 100.0000000 14.4646685 < 0.260 -4.4555359 -4.2200000 100.0000000 14.6023102 < 0.262 -4.4578559 -4.2140000 100.0000000 14.7461277 < 0.264 -4.4549246 -4.2080000 100.0000000 14.8933619 < 0.266 -4.4456232 -4.2020000 100.0000000 15.0405263 < 0.268 -4.4297848 -4.1960000 100.0000000 15.1837487 < 0.270 -4.4072753 -4.1900000 100.0000000 15.3190668 < 0.272 -4.3832487 -4.1840000 100.0000000 15.4440240 < 0.274 -4.3606951 -4.1780000 100.0000000 15.5586072 < 0.276 -4.3454499 -4.1720000 100.0000000 15.6654507 < 0.278 -4.3366430 -4.1660000 100.0000000 15.7686786 < 0.280 -4.3351090 -4.1600000 100.0000000 15.8724042 < 0.282 -4.3410874 -4.1540000 100.0000000 15.9810631 < 0.284 -4.3523721 -4.1480000 100.0000000 16.0985010 < 0.286 -4.3677096 -4.1420000 100.0000000 16.2275256 < 0.288 -4.3789653 -4.1360000 100.0000000 16.3681281 < 0.290 -4.3838354 -4.1300000 100.0000000 16.5171683 < 0.292 -4.3805708 -4.1240000 100.0000000 16.6702901 < 0.294 -4.3677099 -4.1180000 100.0000000 16.8221744 < 0.296 -4.3488621 -4.1120000 100.0000000 16.9681460 < 0.298 -4.3247319 -4.1060000 100.0000000 17.1048242 < 0.300 -4.2979661 -4.1000000 100.0000000 17.2298336 < 0.302 -4.2704359 -4.0940000 100.0000000 17.3421543 < 0.304 -4.2459380 -4.0880000 100.0000000 17.4424665 < 0.306 -4.2253547 -4.0820000 100.0000000 17.5328543 < 0.308 -4.2087629 -4.0760000 100.0000000 17.6156896 < 0.310 -4.1935730 -4.0700000 100.0000000 17.6925904 < 0.312 -4.1806716 -4.0640000 100.0000000 17.7646638 < 0.314 -4.1751363 -4.0580000 100.0000000 17.8348062 < 0.316 -4.1780040 -4.0520000 100.0000000 17.9077483 < 0.318 -4.1919481 -4.0460000 100.0000000 17.9893340 < 0.320 -4.2146149 -4.0400000 100.0000000 18.0855029 < 0.322 -4.2412013 -4.0340000 100.0000000 18.2000478 < 0.324 -4.2665819 -4.0280000 100.0000000 18.3337828 < 0.326 -4.2823640 -4.0220000 100.0000000 18.4834666 < 0.328 -4.2891833 -4.0160000 100.0000000 18.6435308 < 0.330 -4.2838809 -4.0100000 100.0000000 18.8076501 < 0.332 -4.2677198 -4.0040000 100.0000000 18.9689303 < 0.334 -4.2405167 -4.0000000 100.0000000 19.0697776 < 0.336 -4.2083232 -4.0000000 100.0000000 19.0697776 < 0.338 -4.1770975 -4.0000000 100.0000000 19.0697776 < 0.340 -4.1569582 -4.0000000 100.0000000 19.0697776 < 0.342 -4.1502714 -4.0000000 100.0000000 19.0697776 < 0.344 -4.1555572 -4.0000000 100.0000000 19.0697776 < 0.346 -4.1683698 -4.0000000 100.0000000 19.0697776 < 0.348 -4.1800066 -4.0000000 100.0000000 19.0697776 < 0.350 -4.1851354 -4.0000000 100.0000000 19.0697776 < 0.352 -4.1827527 -4.0000000 100.0000000 19.0697776 < 0.354 -4.1723271 -4.0000000 100.0000000 19.0697776 < 0.356 -4.1556508 -4.0000000 100.0000000 19.0697776 < 0.358 -4.1392253 -4.0000000 100.0000000 19.0697776 < 0.360 -4.1286086 -4.0000000 100.0000000 19.0697776 < 0.362 -4.1275393 -4.0000000 100.0000000 19.0697776 < 0.364 -4.1306980 -4.0000000 100.0000000 19.0697776 < 0.366 -4.1358331 -4.0000000 100.0000000 19.0697776 < 0.368 -4.1403863 -4.0000000 100.0000000 19.0697776 < 0.370 -4.1403323 -4.0000000 100.0000000 19.0697776 < 0.372 -4.1355529 -4.0000000 100.0000000 19.0697776 < 0.374 -4.1275167 -4.0000000 100.0000000 19.0697776 < 0.376 -4.1220420 -4.0000000 100.0000000 19.0697776 < 0.378 -4.1207484 -4.0000000 100.0000000 19.0697776 < 0.380 -4.1223525 -4.0000000 100.0000000 19.0697776 < 0.382 -4.1303933 -4.0000000 100.0000000 19.0697776 < 0.384 -4.1463298 -4.0000000 100.0000000 19.0697776 < 0.386 -4.1665813 -4.0000000 100.0000000 19.0697776 < 0.388 -4.1886229 -4.0000000 100.0000000 19.0697776 < 0.390 -4.2100814 -4.0000000 100.0000000 19.0697776 < 0.392 -4.2290019 -4.0000000 100.0000000 19.0697776 < 0.394 -4.2393995 -4.0000000 100.0000000 19.0697776 < 0.396 -4.2409445 -4.0000000 100.0000000 19.0697776 < 0.398 -4.2359552 -4.0000000 100.0000000 19.0697776 < 0.400 -4.2295045 -4.0000000 100.0000000 19.0697776 < 0.402 -4.2228752 -4.0000000 100.0000000 19.0697776 < 0.404 -4.2165714 -4.0000000 100.0000000 19.0697776 < 0.406 -4.2097353 -4.0000000 100.0000000 19.0697776 < 0.408 -4.2003167 -4.0000000 100.0000000 19.0697776 < 0.410 -4.1860241 -4.0000000 100.0000000 19.0697776 < 0.412 -4.1680047 -4.0000000 100.0000000 19.0697776 < 0.414 -4.1455890 -4.0000000 100.0000000 19.0697776 < 0.416 -4.1237576 -4.0000000 100.0000000 19.0697776 < 0.418 -4.1021729 -4.0000000 100.0000000 19.0697776 < 0.420 -4.0819189 -4.0000000 100.0000000 19.0697776 < 0.422 -4.0615600 -4.0000000 100.0000000 19.0697776 < 0.424 -4.0424365 -4.0000000 100.0000000 19.0697776 < 0.426 -4.0306874 -4.0000000 100.0000000 19.0697776 < 0.428 -4.0266546 -4.0000000 100.0000000 19.0697776 < 0.430 -4.0314729 -4.0000000 100.0000000 19.0697776 < 0.432 -4.0445185 -4.0000000 100.0000000 19.0697776 < 0.434 -4.0617575 -4.0000000 100.0000000 19.0697776 < 0.436 -4.0805534 -4.0000000 100.0000000 19.0697776 < 0.438 -4.0958736 -4.0000000 100.0000000 19.0697776 < 0.440 -4.1061057 -4.0000000 100.0000000 19.0697776 < 0.442 -4.1098508 -4.0000000 100.0000000 19.0697776 < 0.444 -4.1121150 -4.0000000 100.0000000 19.0697776 < 0.446 -4.1122438 -4.0000000 100.0000000 19.0697776 < 0.448 -4.1094950 -4.0000000 100.0000000 19.0697776 < 0.450 -4.1073475 -4.0000000 100.0000000 19.0697776 < 0.452 -4.1093988 -4.0000000 100.0000000 19.0697776 < 0.454 -4.1160671 -4.0000000 100.0000000 19.0697776 < 0.456 -4.1299202 -4.0000000 100.0000000 19.0697776 < 0.458 -4.1445674 -4.0000000 100.0000000 19.0697776 < 0.460 -4.1600454 -4.0000000 100.0000000 19.0697776 < 0.462 -4.1722968 -4.0000000 100.0000000 19.0697776 < 0.464 -4.1804451 -4.0000000 100.0000000 19.0697776 < 0.466 -4.1848917 -4.0000000 100.0000000 19.0697776 < 0.468 -4.1847991 -4.0000000 100.0000000 19.0697776 < 0.470 -4.1809254 -4.0000000 100.0000000 19.0697776 < 0.472 -4.1746965 -4.0000000 100.0000000 19.0697776 < 0.474 -4.1677287 -4.0000000 100.0000000 19.0697776 < 0.476 -4.1614391 -4.0000000 100.0000000 19.0697776 < 0.478 -4.1575764 -4.0000000 100.0000000 19.0697776 < 0.480 -4.1577678 -4.0000000 100.0000000 19.0697776 < 0.482 -4.1624254 -4.0000000 100.0000000 19.0697776 < 0.484 -4.1661994 -4.0000000 100.0000000 19.0697776 < 0.486 -4.1683485 -4.0000000 100.0000000 19.0697776 < 0.488 -4.1696030 -4.0000000 100.0000000 19.0697776 < 0.490 -4.1653804 -4.0000000 100.0000000 19.0697776 < 0.492 -4.1544527 -4.0000000 100.0000000 19.0697776 < 0.494 -4.1436747 -4.0000000 100.0000000 19.0697776 < 0.496 -4.1337077 -4.0000000 100.0000000 19.0697776 < 0.498 -4.1242068 -4.0000000 100.0000000 19.0697776 < 0.500 -4.1153626 -4.0000000 100.0000000 19.0697776 < 0.502 -4.1091771 -4.0000000 100.0000000 19.0697776 < 0.504 -4.1029954 -4.0000000 100.0000000 19.0697776 < 0.506 -4.0955021 -4.0000000 100.0000000 19.0697776 < 0.508 -4.0895621 -4.0000000 100.0000000 19.0697776 < 0.510 -4.0890285 -4.0000000 100.0000000 19.0697776 < 0.512 -4.0993501 -4.0000000 100.0000000 19.0697776 < 0.514 -4.1217943 -4.0000000 100.0000000 19.0697776 < 0.516 -4.1528914 -4.0000000 100.0000000 19.0697776 < 0.518 -4.1878656 -4.0000000 100.0000000 19.0697776 < 0.520 -4.2244824 -4.0000000 100.0000000 19.0697776 < 0.522 -4.2566940 -4.0000000 100.0000000 19.0697776 < 0.524 -4.2859702 -4.0000000 100.0000000 19.0697776 < 0.526 -4.3102890 -4.0000000 100.0000000 19.0697776 < 0.528 -4.3279937 -4.0000000 100.0000000 19.0697776 < 0.530 -4.3360295 -4.0000000 100.0000000 19.0697776 < 0.532 -4.3348344 -4.0000000 100.0000000 19.0697776 < 0.534 -4.3237465 -4.0000000 100.0000000 19.0697776 < 0.536 -4.3040426 -4.0000000 100.0000000 19.0697776 < 0.538 -4.2776031 -4.0000000 100.0000000 19.0697776 < 0.540 -4.2468833 -4.0000000 100.0000000 19.0697776 < 0.542 -4.2114110 -4.0000000 100.0000000 19.0697776 < 0.544 -4.1758548 -4.0000000 100.0000000 19.0697776 < 0.546 -4.1442003 -4.0000000 100.0000000 19.0697776 < 0.548 -4.1184276 -4.0000000 100.0000000 19.0697776 < 0.550 -4.1008409 -4.0000000 100.0000000 19.0697776 < 0.552 -4.0948106 -4.0000000 100.0000000 19.0697776 < 0.554 -4.1021824 -4.0000000 100.0000000 19.0697776 < 0.556 -4.1248085 -4.0000000 100.0000000 19.0697776 < 0.558 -4.1573676 -4.0000000 100.0000000 19.0697776 < 0.560 -4.1954410 -4.0000000 100.0000000 19.0697776 < 0.562 -4.2329640 -4.0000000 100.0000000 19.0697776 < 0.564 -4.2637623 -4.0000000 100.0000000 19.0697776 < 0.566 -4.2854478 -4.0000000 100.0000000 19.0697776 < 0.568 -4.2964571 -4.0000000 100.0000000 19.0697776 < 0.570 -4.2967035 -4.0000000 100.0000000 19.0697776 < 0.572 -4.2858108 -4.0000000 100.0000000 19.0697776 < 0.574 -4.2683232 -4.0000000 100.0000000 19.0697776 < 0.576 -4.2454422 -4.0000000 100.0000000 19.0697776 < 0.578 -4.2192533 -4.0000000 100.0000000 19.0697776 < 0.580 -4.1949911 -4.0000000 100.0000000 19.0697776 < 0.582 -4.1745677 -4.0000000 100.0000000 19.0697776 < 0.584 -4.1621328 -4.0000000 100.0000000 19.0697776 < 0.586 -4.1534278 -4.0000000 100.0000000 19.0697776 < 0.588 -4.1458530 -4.0000000 100.0000000 19.0697776 < 0.590 -4.1341725 -4.0000000 100.0000000 19.0697776 < 0.592 -4.1149900 -4.0000000 100.0000000 19.0697776 < 0.594 -4.0890991 -4.0000000 100.0000000 19.0697776 < 0.596 -4.0615742 -4.0000000 100.0000000 19.0697776 < 0.598 -4.0385222 -4.0000000 100.0000000 19.0697776 < 0.600 -4.0288166 -4.0000000 100.0000000 19.0697776 < 0.602 -4.0395353 -4.0000000 100.0000000 19.0697776 < 0.604 -4.0676232 -4.0000000 100.0000000 19.0697776 < 0.606 -4.1099974 -4.0000000 100.0000000 19.0697776 < 0.608 -4.1589252 -4.0000000 100.0000000 19.0697776 < 0.610 -4.2070553 -4.0000000 100.0000000 19.0697776 < 0.612 -4.2499782 -4.0000000 100.0000000 19.0697776 < 0.614 -4.2840456 -4.0000000 100.0000000 19.0697776 < 0.616 -4.3087251 -4.0000000 100.0000000 19.0697776 < 0.618 -4.3234970 -4.0000000 100.0000000 19.0697776 < 0.620 -4.3288165 -4.0000000 100.0000000 19.0697776 < 0.622 -4.3271900 -4.0000000 100.0000000 19.0697776 < 0.624 -4.3216460 -4.0000000 100.0000000 19.0697776 < 0.626 -4.3163752 -4.0000000 100.0000000 19.0697776 < 0.628 -4.3110518 -4.0000000 100.0000000 19.0697776 < 0.630 -4.3045374 -4.0000000 100.0000000 19.0697776 < 0.632 -4.2946516 -4.0000000 100.0000000 19.0697776 < 0.634 -4.2822018 -4.0000000 100.0000000 19.0697776 < 0.636 -4.2678504 -4.0000000 100.0000000 19.0697776 < 0.638 -4.2537900 -4.0000000 100.0000000 19.0697776 < 0.640 -4.2430402 -4.0000000 100.0000000 19.0697776 < 0.642 -4.2361480 -4.0000000 100.0000000 19.0697776 < 0.644 -4.2316854 -4.0000000 100.0000000 19.0697776 < 0.646 -4.2256472 -4.0000000 100.0000000 19.0697776 < 0.648 -4.2180196 -4.0000000 100.0000000 19.0697776 < 0.650 -4.2091294 -4.0000000 100.0000000 19.0697776 < 0.652 -4.1961629 -4.0000000 100.0000000 19.0697776 < 0.654 -4.1788260 -4.0000000 100.0000000 19.0697776 < 0.656 -4.1599399 -4.0000000 100.0000000 19.0697776 < 0.658 -4.1466299 -4.0000000 100.0000000 19.0697776 < 0.660 -4.1454697 -4.0000000 100.0000000 19.0697776 < 0.662 -4.1609005 -4.0000000 100.0000000 19.0697776 < 0.664 -4.1919619 -4.0000000 100.0000000 19.0697776 < 0.666 -4.2327798 -4.0000000 100.0000000 19.0697776 < 0.668 -4.2759411 -4.0040000 100.0000000 18.9688334 < 0.670 -4.3125460 -4.0100000 100.0000000 18.7964873 < 0.672 -4.3341484 -4.0160000 100.0000000 18.6102789 < 0.674 -4.3392942 -4.0220000 100.0000000 18.4196461 < 0.676 -4.3311983 -4.0280000 100.0000000 18.2334983 < 0.678 -4.3119785 -4.0340000 100.0000000 18.0591452 < 0.680 -4.2884199 -4.0400000 100.0000000 17.9012256 < 0.682 -4.2673909 -4.0460000 100.0000000 17.7602824 < 0.684 -4.2580229 -4.0520000 100.0000000 17.6320582 < 0.686 -4.2619607 -4.0580000 100.0000000 17.5090631 < 0.688 -4.2787423 -4.0640000 100.0000000 17.3834521 < 0.690 -4.2961749 -4.0700000 100.0000000 17.2511769 < 0.692 -4.3075286 -4.0760000 100.0000000 17.1138659 < 0.694 -4.3070496 -4.0820000 100.0000000 16.9768924 < 0.696 -4.2952236 -4.0880000 100.0000000 16.8472104 < 0.698 -4.2768719 -4.0940000 100.0000000 16.7301817 < 0.700 -4.2626307 -4.1000000 100.0000000 16.6265309 < 0.702 -4.2573864 -4.1060000 100.0000000 16.5323257 < 0.704 -4.2613714 -4.1120000 100.0000000 16.4420984 < 0.706 -4.2758450 -4.1180000 100.0000000 16.3499334 < 0.708 -4.2986314 -4.1240000 100.0000000 16.2501904 < 0.710 -4.3224349 -4.1300000 100.0000000 16.1400705 < 0.712 -4.3408431 -4.1360000 100.0000000 16.0208871 < 0.714 -4.3486789 -4.1420000 100.0000000 15.8974304 < 0.716 -4.3396743 -4.1480000 100.0000000 15.7779244 < 0.718 -4.3164636 -4.1540000 100.0000000 15.6716831 < 0.720 -4.2808726 -4.1600000 100.0000000 15.5866822 < 0.722 -4.2408933 -4.1660000 100.0000000 15.5279524 < 0.724 -4.2092773 -4.1720000 100.0000000 15.4943012 < 0.726 -4.1941533 -4.1780000 100.0000000 15.4782720 < 0.728 -4.2033836 -4.1840000 100.0000000 15.4676109 < 0.730 -4.2314577 -4.1900000 100.0000000 15.4493584 < 0.732 -4.2653861 -4.1960000 100.0000000 15.4161053 < 0.734 -4.2948715 -4.2020000 100.0000000 15.3674280 < 0.736 -4.3152391 -4.2080000 100.0000000 15.3073947 < 0.738 -4.3259785 -4.2140000 100.0000000 15.2416294 < 0.740 -4.3315871 -4.2200000 100.0000000 15.1745597 < 0.742 -4.3373100 -4.2260000 100.0000000 15.1076905 < 0.744 -4.3475564 -4.2320000 100.0000000 15.0396306 < 0.746 -4.3645604 -4.2380000 100.0000000 14.9669955 < 0.748 -4.3897805 -4.2440000 100.0000000 14.8852932 < 0.750 -4.4185465 -4.2500000 100.0000000 14.7909951 < 0.752 -4.4456323 -4.2560000 100.0000000 14.6835414 < 0.754 -4.4673709 -4.2620000 100.0000000 14.5650405 < 0.756 -4.4830698 -4.2680000 100.0000000 14.4389082 < 0.758 -4.4920483 -4.2740000 100.0000000 14.3089728 < 0.760 -4.4946955 -4.2800000 100.0000000 14.1791496 < 0.762 -4.4914523 -4.2860000 100.0000000 14.0531052 < 0.764 -4.4830334 -4.2920000 100.0000000 13.9341595 < 0.766 -4.4730692 -4.2980000 100.0000000 13.8243287 < 0.768 -4.4662419 -4.3040000 100.0000000 13.7231354 < 0.770 -4.4633868 -4.3100000 100.0000000 13.6284467 < 0.772 -4.4625553 -4.3160000 100.0000000 13.5384641 < 0.774 -4.4612265 -4.3220000 100.0000000 13.4527295 < 0.776 -4.4569238 -4.3280000 100.0000000 13.3722844 < 0.778 -4.4495559 -4.3340000 100.0000000 13.2989405 < 0.780 -4.4389431 -4.3400000 100.0000000 13.2345907 < 0.782 -4.4259776 -4.3460000 100.0000000 13.1809145 < 0.784 -4.4150891 -4.3520000 100.0000000 13.1379945 < 0.786 -4.4078927 -4.3580000 100.0000000 13.1040999 < 0.788 -4.4054166 -4.3640000 100.0000000 13.0767071 < 0.790 -4.4085914 -4.3700000 100.0000000 13.0527047 < 0.792 -4.4145164 -4.3760000 100.0000000 13.0295723 < 0.794 -4.4232163 -4.3820000 100.0000000 13.0056524 < 0.796 -4.4331492 -4.3880000 100.0000000 12.9797427 < 0.798 -4.4427998 -4.3940000 100.0000000 12.9515580 < 0.800 -4.4545447 -4.4000000 100.0000000 12.9205546 < 0.802 -4.4680949 -4.4060000 100.0000000 12.8855627 < 0.804 -4.4814617 -4.4120000 100.0000000 12.8460957 < 0.806 -4.4932579 -4.4180000 100.0000000 12.8026798 < 0.808 -4.5043306 -4.4240000 100.0000000 12.7560032 < 0.810 -4.5124727 -4.4300000 100.0000000 12.7071622 < 0.812 -4.5177074 -4.4360000 100.0000000 12.6579081 < 0.814 -4.5213563 -4.4420000 100.0000000 12.6095890 < 0.816 -4.5216608 -4.4480000 100.0000000 12.5636838 < 0.818 -4.5187037 -4.4540000 100.0000000 12.5221745 < 0.820 -4.5106892 -4.4600000 100.0000000 12.4875566 < 0.822 -4.5023840 -4.4660000 100.0000000 12.4614346 < 0.824 -4.4964887 -4.4720000 100.0000000 12.4431728 < 0.826 -4.4963003 -4.4780000 100.0000000 12.4303360 < 0.828 -4.5043280 -4.4840000 100.0000000 12.4187475 < 0.830 -4.5209824 -4.4900000 100.0000000 12.4033543 < 0.832 -4.5429366 -4.4960000 100.0000000 12.3799786 < 0.834 -4.5684978 -4.5020000 100.0000000 12.3459482 < 0.836 -4.5940559 -4.5080000 100.0000000 12.3001821 < 0.838 -4.6168832 -4.5140000 100.0000000 12.2435004 < 0.840 -4.6375751 -4.5200000 100.0000000 12.1773628 < 0.842 -4.6539226 -4.5260000 100.0000000 12.1037135 < 0.844 -4.6674650 -4.5320000 100.0000000 12.0246972 < 0.846 -4.6829956 -4.5380000 100.0000000 11.9405590 < 0.848 -4.7013998 -4.5440000 100.0000000 11.8498404 < 0.850 -4.7233373 -4.5500000 100.0000000 11.7506192 < 0.852 -4.7465023 -4.5560000 100.0000000 11.6414673 < 0.854 -4.7704339 -4.5620000 100.0000000 11.5217864 < 0.856 -4.7907813 -4.5680000 100.0000000 11.3924218 < 0.858 -4.8066020 -4.5740000 100.0000000 11.2558068 < 0.860 -4.8159132 -4.5800000 100.0000000 11.1152522 < 0.862 -4.8190359 -4.5860000 100.0000000 10.9745675 < 0.864 -4.8168330 -4.5920000 100.0000000 10.8372068 < 0.866 -4.8107176 -4.5980000 100.0000000 10.7059416 < 0.868 -4.8015071 -4.6040000 100.0000000 10.5828741 < 0.870 -4.7921970 -4.6100000 100.0000000 10.4689628 < 0.872 -4.7841801 -4.6160000 100.0000000 10.3638497 < 0.874 -4.7801702 -4.6220000 100.0000000 10.2659445 < 0.876 -4.7821503 -4.6280000 100.0000000 10.1722484 < 0.878 -4.7903296 -4.6340000 100.0000000 10.0791044 < 0.880 -4.8022025 -4.6400000 100.0000000 9.9835447 < 0.882 -4.8162695 -4.6460000 100.0000000 9.8838031 < 0.884 -4.8303312 -4.6520000 100.0000000 9.7792228 < 0.886 -4.8427185 -4.6580000 100.0000000 9.6703079 < 0.888 -4.8516251 -4.6640000 100.0000000 9.5586048 < 0.890 -4.8567872 -4.6700000 100.0000000 9.4462811 < 0.892 -4.8589383 -4.6760000 100.0000000 9.3353634 < 0.894 -4.8600466 -4.6820000 100.0000000 9.2270679 < 0.896 -4.8624470 -4.6880000 100.0000000 9.1213198 < 0.898 -4.8681479 -4.6940000 100.0000000 9.0167413 < 0.900 -4.8779950 -4.7000000 100.0000000 8.9110984 < 0.902 -4.8913805 -4.7060000 100.0000000 8.8020857 < 0.904 -4.9064610 -4.7120000 100.0000000 8.6881332 < 0.906 -4.9200762 -4.7180000 100.0000000 8.5691721 < 0.908 -4.9305017 -4.7240000 100.0000000 8.4465987 < 0.910 -4.9360604 -4.7300000 100.0000000 8.3228300 < 0.912 -4.9370601 -4.7360000 100.0000000 8.2006939 < 0.914 -4.9348059 -4.7420000 100.0000000 8.0825340 < 0.916 -4.9309943 -4.7480000 100.0000000 7.9697940 < 0.918 -4.9282684 -4.7540000 100.0000000 7.8626152 < 0.920 -4.9277825 -4.7600000 100.0000000 7.7599999 < 0.922 -4.9303875 -4.7660000 100.0000000 7.6603488 < 0.924 -4.9351099 -4.7720000 100.0000000 7.5620996 < 0.926 -4.9412416 -4.7780000 100.0000000 7.4641941 < 0.928 -4.9473764 -4.7840000 100.0000000 7.3662087 < 0.930 -4.9516003 -4.7900000 100.0000000 7.2687156 < 0.932 -4.9527616 -4.7960000 100.0000000 7.1732070 < 0.934 -4.9501528 -4.8020000 100.0000000 7.0817327 < 0.936 -4.9436326 -4.8080000 100.0000000 6.9965970 < 0.938 -4.9340249 -4.8140000 100.0000000 6.9198998 < 0.940 -4.9236089 -4.8200000 100.0000000 6.8528096 < 0.942 -4.9147828 -4.8260000 100.0000000 6.7950921 < 0.944 -4.9088710 -4.8320000 100.0000000 6.7453959 < 0.946 -4.9067932 -4.8380000 100.0000000 6.7016966 < 0.948 -4.9077343 -4.8440000 100.0000000 6.6619383 < 0.950 -4.9105194 -4.8500000 100.0000000 6.6246622 < 0.952 -4.9146198 -4.8560000 100.0000000 6.5889204 < 0.954 -4.9196663 -4.8620000 100.0000000 6.5540345 < 0.956 -4.9252389 -4.8680000 100.0000000 6.5195629 < 0.958 -4.9316168 -4.8740000 100.0000000 6.4851061 < 0.960 -4.9380095 -4.8800000 100.0000000 6.4504182 < 0.962 -4.9431824 -4.8860000 100.0000000 6.4158606 < 0.964 -4.9473437 -4.8920000 100.0000000 6.3821027 < 0.966 -4.9507275 -4.8980000 100.0000000 6.3496814 < 0.968 -4.9531707 -4.9040000 100.0000000 6.3191119 < 0.970 -4.9553990 -4.9100000 100.0000000 6.2907410 < 0.972 -4.9564611 -4.9160000 100.0000000 6.2649829 < 0.974 -4.9559909 -4.9220000 100.0000000 6.2426473 < 0.976 -4.9545507 -4.9280000 100.0000000 6.2244848 < 0.978 -4.9524788 -4.9340000 100.0000000 6.2109759 < 0.980 -4.9507729 -4.9400000 100.0000000 6.2022004 < 0.982 -4.9503707 -4.9460000 100.0000000 6.1976573 < 0.984 -4.9513533 -4.9520000 100.0000000 6.1965400 < 0.986 -4.9540213 -4.9580000 100.0000000 6.1979276 < 0.988 -4.9581577 -4.9640000 100.0000000 6.2008739 < 0.990 -4.9628894 -4.9700000 100.0000000 6.2047597 < 0.992 -4.9677695 -4.9760000 100.0000000 6.2093620 < 0.994 -4.9720206 -4.9820000 100.0000000 6.2148250 < 0.996 -4.9746754 -4.9880000 100.0000000 6.2218162 < 0.998 -4.9756532 -4.9940000 100.0000000 6.2313175 < # < # <> total work done: 6.231317573 < # --------------------------------------- possible FAILURE: check rem.log.dif /home/makoto/amber12/test/ncsu/premd 1,56d0 < # Replica Exchange log file < # numexchg is 10 < # REMD filenames: < # remlog= rem.log < # remtype= rem.type < # Rep#, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate (i,i+1), ResStruct# < # exchange 1 < 1 -1.00 0. -10152.55 320.00 320.00 0. -1 < 2 -1.00 0. -10313.68 300.00 300.00 0. -1 < 3 -1.00 0. -10131.41 330.00 330.00 0. -1 < 4 -1.00 0. -10184.84 310.00 310.00 0. -1 < # exchange 2 < 1 -1.00 308.46 -10128.95 320.00 320.00 0. -1 < 2 -1.00 295.33 -10317.63 300.00 300.00 0. -1 < 3 -1.00 309.55 -10093.02 330.00 330.00 0. -1 < 4 -1.00 301.86 -10230.52 310.00 310.00 0. -1 < # exchange 3 < 1 -1.00 308.74 -10155.85 320.00 320.00 0. -1 < 2 -1.00 289.65 -10277.29 300.00 300.00 0. -1 < 3 -1.00 303.44 -10069.64 330.00 330.00 0. -1 < 4 -1.00 294.86 -10165.38 310.00 310.00 0. -1 < # exchange 4 < 1 -1.00 313.60 -10164.50 320.00 320.00 0. -1 < 2 -1.00 285.00 -10250.62 300.00 300.00 0. -1 < 3 -1.00 307.50 -10076.25 330.00 330.00 0. -1 < 4 -1.00 291.94 -10166.22 310.00 310.00 0. -1 < # exchange 5 < 1 -1.00 308.93 -10147.18 320.00 320.00 0. -1 < 2 -1.00 290.54 -10294.49 300.00 300.00 0. -1 < 3 -1.00 304.21 -10073.01 330.00 330.00 0. -1 < 4 -1.00 292.64 -10165.84 310.00 310.00 0. -1 < # exchange 6 < 1 -1.00 306.64 -10125.62 320.00 320.00 0. -1 < 2 -1.00 288.34 -10257.34 300.00 300.00 0. -1 < 3 -1.00 310.27 -10105.01 330.00 330.00 0. -1 < 4 -1.00 299.16 -10192.37 310.00 310.00 0. -1 < # exchange 7 < 1 -1.00 302.08 -10095.57 320.00 320.00 0. -1 < 2 -1.00 283.39 -10240.54 300.00 300.00 0. -1 < 3 -1.00 306.46 -10081.57 330.00 330.00 0. -1 < 4 -1.00 296.58 -10186.97 310.00 310.00 0. -1 < # exchange 8 < 1 -1.00 299.23 -10078.43 320.00 320.00 0. -1 < 2 1.02 283.51 -10236.66 300.00 310.00 0.25 -1 < 3 -1.00 308.20 -10080.62 330.00 330.00 0. -1 < 4 0.98 301.32 -10202.87 310.00 300.00 0. -1 < # exchange 9 < 1 -1.00 295.30 -10054.41 320.00 320.00 0. -1 < 2 -1.00 292.68 -10238.31 310.00 310.00 0. -1 < 3 -1.00 311.45 -10117.38 330.00 330.00 0. -1 < 4 -1.00 288.00 -10199.33 300.00 300.00 0.22 -1 < # exchange 10 < 1 -1.00 298.26 -10079.60 320.00 320.00 0. -1 < 2 -1.00 290.34 -10217.17 310.00 310.00 0. -1 < 3 -1.00 309.27 -10081.68 330.00 330.00 0. -1 < 4 -1.00 293.44 -10222.59 300.00 300.00 0.20 -1 --------------------------------------- possible FAILURE: check ncsu-pmd.log.dif /home/makoto/amber12/test/ncsu/premd 1,73d0 < ******************************************************************************** < REPLICA #0 (temp0 = 320.000) < MDIN = 'mdin.3' < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < NCSU : < NCSU : output_file = pmd.3.txt < NCSU : output_freq = 1 (0.0020 ps) < NCSU : < NCSU : CV #1 << anchor : position = 7.000000, strength = 3.000000 >> < NCSU : type = 'R_OF_GYRATION' < NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], < NCSU : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], < NCSU : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], < NCSU : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], < NCSU : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], < NCSU : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) < NCSU : < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < ******************************************************************************** < REPLICA #1 (temp0 = 300.000) < MDIN = 'mdin.1' < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < NCSU : < NCSU : output_file = pmd.1.txt < NCSU : output_freq = 1 (0.0020 ps) < NCSU : < NCSU : CV #1 << anchor : position = 5.000000, strength = 1.000000 >> < NCSU : type = 'R_OF_GYRATION' < NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], < NCSU : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], < NCSU : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], < NCSU : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], < NCSU : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], < NCSU : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) < NCSU : < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < ******************************************************************************** < REPLICA #2 (temp0 = 330.000) < MDIN = 'mdin.4' < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < NCSU : < NCSU : output_file = pmd.4.txt < NCSU : output_freq = 1 (0.0020 ps) < NCSU : < NCSU : CV #1 << anchor : position = 8.000000, strength = 4.000000 >> < NCSU : type = 'R_OF_GYRATION' < NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], < NCSU : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], < NCSU : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], < NCSU : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], < NCSU : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], < NCSU : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) < NCSU : < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < ******************************************************************************** < REPLICA #3 (temp0 = 310.000) < MDIN = 'mdin.2' < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ P I N N E D M.D. ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < NCSU : < NCSU : output_file = pmd.2.txt < NCSU : output_freq = 1 (0.0020 ps) < NCSU : < NCSU : CV #1 << anchor : position = 6.000000, strength = 2.000000 >> < NCSU : type = 'R_OF_GYRATION' < NCSU : atoms = (1 [N], 5 [CA], 8 [C], 10 [N], 12 [CA], < NCSU : 29 [C], 31 [N], 33 [CA], 41 [C], 43 [N], < NCSU : 53 [CA], 55 [C], 57 [N], 59 [CA], 70 [C], < NCSU : 72 [N], 74 [CA], 84 [C], 86 [N], 88 [CA], < NCSU : 91 [C], 93 [N], 95 [CA], 105 [C], 107 [N], < NCSU : 109 [CA], 129 [C], 131 [N], 133 [CA], 136 [C]) < NCSU : < NCSU : ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ < ******************************************************************************** --------------------------------------- possible FAILURE: check pmd.1.txt.dif /home/makoto/amber12/test/ncsu/premd 1,65d0 < # = NCSU%PMD ================================================================== < # << anchor(1) : position = 5.00000, strength = 1.00000 >> < # ----------------------------------------------------------------------------- < # MD time (ps), CV(1:1) < # ============================================================================= < 0. 7.3651005 < 0.002 7.3640012 < 0.004 7.3629364 < 0.006 7.3617774 < 0.008 7.3604180 < 0.010 7.3588226 < 0.010 7.3588226 < 0.012 7.3570335 < 0.014 7.3551367 < 0.016 7.3532191 < 0.018 7.3513475 < 0.020 7.3495676 < 0.020 7.3495676 < 0.022 7.3478948 < 0.024 7.3463040 < 0.026 7.3447373 < 0.028 7.3431298 < 0.030 7.3414287 < 0.030 7.3414287 < 0.032 7.3395946 < 0.034 7.3375893 < 0.036 7.3353719 < 0.038 7.3329064 < 0.040 7.3301806 < 0.040 7.3301806 < 0.042 7.3272159 < 0.044 7.3240552 < 0.046 7.3207359 < 0.048 7.3172750 < 0.050 7.3136797 < 0.050 7.3136797 < 0.052 7.3099683 < 0.054 7.3061836 < 0.056 7.3023853 < 0.058 7.2986312 < 0.060 7.2949694 < 0.060 7.2949694 < 0.062 7.2914564 < 0.064 7.2881680 < 0.066 7.2851606 < 0.068 7.2824125 < 0.070 7.2798247 < 0.070 6.2726156 < 0.072 6.2700099 < 0.074 6.2676750 < 0.076 6.2658457 < 0.078 6.2646304 < 0.080 6.2639706 < 0.080 6.2639706 < 0.082 6.2636764 < 0.084 6.2635229 < 0.086 6.2633525 < 0.088 6.2631342 < 0.090 6.2629655 < 0.090 6.2629655 < 0.092 6.2630234 < 0.094 6.2634758 < 0.096 6.2643922 < 0.098 6.2657099 < 0.100 6.2672772 --------------------------------------- possible FAILURE: check mdout.1.dif /home/makoto/amber12/test/ncsu/premd 1,166d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < [-O]verwriting output < File Assignments: < Here is the input file: < &cntrl < igb = 0, ntx = 7, irest = 1, < ntb = 1, ntp = 0, temp0 = 300., < ntt = 1, gamma_ln = 0., < ntf = 2, ntc = 2, tol = 0.0000, < cut = 8., dt = 0.00, < ntpr = 5, ntwx = 0, nstlim = 5, < numexchg = 10 < / < ncsu_pmd < output_file = 'pmd.1.txt' < output_freq = 1 < variable ! 1 < type = R_OF_GYRATION < i = (1, 5, 8, 10, 12, 29, 31, 33, 41 < , 43, 53, 55, 57, 59, 70, 72, 74, 84, 86 < , 88, 91, 93, 95, 105, 107, 109, 129, 131, 133 < , 136) < anchor_position = 5. < anchor_strength = 1. < end variable < end ncsu_pmd < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting new box info from bottom of inpcrd < NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 < NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 < NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 < NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 < NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 < IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < BOX TYPE: TRUNCATED OCTAHEDRON < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < NGLY < General flags: < imin = 0, nmropt = 0 < Replica exchange < numexchg= 10, rem= 1 < Nature and format of input: < ntx = 7, irest = 1, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 5, ntrx = 1, ntwr = 500 < iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 < ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 1, igb = 0, nsnb = 25 < ipol = 0, gbsa = 0, iesp = 0 < dielc = 1.0000, cut = 8.0000, intdiel = 1.0000 < Frozen or restrained atoms: < ibelly = 0, ntr = 0 < Molecular dynamics: < nstlim = 5, nscm = 1000, nrespa = 1 < t = 0., dt = 0.0020, vlimit = 20.0000 < Berendsen (weak-coupling) temperature regulation: < temp0 = 300.0000, tempi = 0., tautp = 1.0000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0.0000 < Ewald parameters: < verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 < vdwmeth = 1, eedmeth = 1, netfrc = 1 < Box X = 34.47 Box Y = 34.47 Box Z = 34.47 < Alpha = 109.47 Beta = 109.47 Gamma = 109.47 < NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 < Cutoff= 8.00 Tol =0.10E-4 < Ewald Coefficient = 0.3486 < Interpolation order = 4 < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < NGLY < begin time read from input coords = 0. ps < Number of triangulated 3-point waters found: 1001 < Sum of charges from parm topology file = -0.0000000 < Forcing neutrality... < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < --------------------------------------------------- < APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION < using 5000. points per unit in tabled values < TESTING RELATIVE ERROR over r ranging from 0. to cutoff < --------------------------------------------------- < NSTEP = 5 TIME(PS) = 0.01 TEMP(K) = 308.4 PRESS = 0. < Etot = -8191.933 EKtot = 1949.826 EPtot = -10141.760 < BOND = 21.359 ANGLE = 62.992 DIHED = 75.146 < 1-4 NB = 33.295 1-4 EEL = 538.293 VDWAALS = 1413.833 < EELEC = -12286.679 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 1 < ------------------------------------------------------------------------------ < NSTEP = 10 TIME(PS) = 0.02 TEMP(K) = 308.7 PRESS = 0. < Etot = -8190.538 EKtot = 1951.616 EPtot = -10142.154 < BOND = 30.856 ANGLE = 71.745 DIHED = 77.952 < 1-4 NB = 33.253 1-4 EEL = 533.808 VDWAALS = 1411.189 < EELEC = -12300.960 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 2 < ------------------------------------------------------------------------------ < NSTEP = 15 TIME(PS) = 0.03 TEMP(K) = 313.6 PRESS = 0. < Etot = -8190.344 EKtot = 1982.342 EPtot = -10172.687 < BOND = 22.956 ANGLE = 72.386 DIHED = 72.698 < 1-4 NB = 32.463 1-4 EEL = 540.933 VDWAALS = 1413.210 < EELEC = -12327.336 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 3 < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 0.04 TEMP(K) = 308.9 PRESS = 0. < Etot = -8189.096 EKtot = 1952.824 EPtot = -10141.920 < BOND = 30.888 ANGLE = 74.275 DIHED = 75.697 < 1-4 NB = 35.506 1-4 EEL = 541.915 VDWAALS = 1408.325 < EELEC = -12308.530 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 4 < ------------------------------------------------------------------------------ < NSTEP = 25 TIME(PS) = 0.05 TEMP(K) = 306.6 PRESS = 0. < Etot = -8188.270 EKtot = 1938.336 EPtot = -10126.606 < BOND = 31.091 ANGLE = 60.967 DIHED = 79.186 < 1-4 NB = 32.608 1-4 EEL = 541.245 VDWAALS = 1414.046 < EELEC = -12285.751 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 5 < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 0.06 TEMP(K) = 302.0 PRESS = 0. < Etot = -8187.519 EKtot = 1909.528 EPtot = -10097.047 < BOND = 31.823 ANGLE = 61.354 DIHED = 82.768 < 1-4 NB = 34.960 1-4 EEL = 538.148 VDWAALS = 1436.369 < EELEC = -12282.471 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 6 < ------------------------------------------------------------------------------ < NSTEP = 35 TIME(PS) = 0.07 TEMP(K) = 299.2 PRESS = 0. < Etot = -8186.680 EKtot = 1891.514 EPtot = -10078.194 < BOND = 30.374 ANGLE = 61.521 DIHED = 76.827 < 1-4 NB = 36.030 1-4 EEL = 541.766 VDWAALS = 1434.348 < EELEC = -12259.064 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 7 < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 0.08 TEMP(K) = 295.3 PRESS = 0. < Etot = -8185.209 EKtot = 1866.676 EPtot = -10051.885 < BOND = 22.428 ANGLE = 69.716 DIHED = 77.462 < 1-4 NB = 39.163 1-4 EEL = 536.508 VDWAALS = 1386.384 < EELEC = -12183.548 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 8 < ------------------------------------------------------------------------------ < NSTEP = 45 TIME(PS) = 0.09 TEMP(K) = 298.2 PRESS = 0. < Etot = -8183.752 EKtot = 1885.362 EPtot = -10069.115 < BOND = 25.450 ANGLE = 74.505 DIHED = 76.615 < 1-4 NB = 38.756 1-4 EEL = 537.473 VDWAALS = 1326.886 < EELEC = -12148.803 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 9 < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 307.1 PRESS = 0. < Etot = -8183.348 EKtot = 1941.824 EPtot = -10125.173 < BOND = 24.436 ANGLE = 66.152 DIHED = 71.801 < 1-4 NB = 34.650 1-4 EEL = 539.467 VDWAALS = 1300.813 < EELEC = -12162.495 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 320.000 REPNUM = 1 EXCHANGE# = 10 < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --------------------------------------- possible FAILURE: check pmd.2.txt.dif /home/makoto/amber12/test/ncsu/premd 1,65d0 < # = NCSU%PMD ================================================================== < # << anchor(1) : position = 6.00000, strength = 2.00000 >> < # ----------------------------------------------------------------------------- < # MD time (ps), CV(1:1) < # ============================================================================= < 0. 6.3043274 < 0.002 6.3051974 < 0.004 6.3060366 < 0.006 6.3065837 < 0.008 6.3066496 < 0.010 6.3062246 < 0.010 6.3062246 < 0.012 6.3054831 < 0.014 6.3046736 < 0.016 6.3039966 < 0.018 6.3035608 < 0.020 6.3033904 < 0.020 6.3033904 < 0.022 6.3034209 < 0.024 6.3034852 < 0.026 6.3033503 < 0.028 6.3028164 < 0.030 6.3018199 < 0.030 6.3018199 < 0.032 6.3004610 < 0.034 6.2989386 < 0.036 6.2974475 < 0.038 6.2961067 < 0.040 6.2949479 < 0.040 6.2949479 < 0.042 6.2939361 < 0.044 6.2929890 < 0.046 6.2919934 < 0.048 6.2908468 < 0.050 6.2895180 < 0.050 6.2895180 < 0.052 6.2880726 < 0.054 6.2866312 < 0.056 6.2852865 < 0.058 6.2840418 < 0.060 6.2828027 < 0.060 6.2828027 < 0.062 6.2814158 < 0.064 6.2797342 < 0.066 6.2776767 < 0.068 6.2752608 < 0.070 6.2726156 < 0.070 7.2798247 < 0.072 7.2772383 < 0.074 7.2746275 < 0.076 7.2720062 < 0.078 7.2694636 < 0.080 7.2671203 < 0.080 7.2671203 < 0.082 7.2650747 < 0.084 7.2633587 < 0.086 7.2619155 < 0.088 7.2606100 < 0.090 7.2592694 < 0.090 7.2592694 < 0.092 7.2577393 < 0.094 7.2559426 < 0.096 7.2539186 < 0.098 7.2518049 < 0.100 7.2497611 --------------------------------------- possible FAILURE: check mdout.2.dif /home/makoto/amber12/test/ncsu/premd 1,166d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < [-O]verwriting output < File Assignments: < Here is the input file: < &cntrl < igb = 0, ntx = 7, irest = 1, < ntb = 1, ntp = 0, temp0 = 310., < ntt = 1, gamma_ln = 0., < ntf = 2, ntc = 2, tol = 0.0000, < cut = 8., dt = 0.00, < ntpr = 5, ntwx = 0, nstlim = 5, < numexchg = 10 < / < ncsu_pmd < output_file = 'pmd.2.txt' < output_freq = 1 < variable ! 1 < type = R_OF_GYRATION < i = (1, 5, 8, 10, 12, 29, 31, 33, 41 < , 43, 53, 55, 57, 59, 70, 72, 74, 84, 86 < , 88, 91, 93, 95, 105, 107, 109, 129, 131, 133 < , 136) < anchor_position = 6. < anchor_strength = 2. < end variable < end ncsu_pmd < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting new box info from bottom of inpcrd < NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 < NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 < NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 < NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 < NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 < IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < BOX TYPE: TRUNCATED OCTAHEDRON < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < NGLY < General flags: < imin = 0, nmropt = 0 < Replica exchange < numexchg= 10, rem= 1 < Nature and format of input: < ntx = 7, irest = 1, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 5, ntrx = 1, ntwr = 500 < iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 < ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 1, igb = 0, nsnb = 25 < ipol = 0, gbsa = 0, iesp = 0 < dielc = 1.0000, cut = 8.0000, intdiel = 1.0000 < Frozen or restrained atoms: < ibelly = 0, ntr = 0 < Molecular dynamics: < nstlim = 5, nscm = 1000, nrespa = 1 < t = 0., dt = 0.0020, vlimit = 20.0000 < Berendsen (weak-coupling) temperature regulation: < temp0 = 310.0000, tempi = 0., tautp = 1.0000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0.0000 < Ewald parameters: < verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 < vdwmeth = 1, eedmeth = 1, netfrc = 1 < Box X = 34.47 Box Y = 34.47 Box Z = 34.47 < Alpha = 109.47 Beta = 109.47 Gamma = 109.47 < NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 < Cutoff= 8.00 Tol =0.10E-4 < Ewald Coefficient = 0.3486 < Interpolation order = 4 < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < NGLY < begin time read from input coords = 0. ps < Number of triangulated 3-point waters found: 1001 < Sum of charges from parm topology file = -0.0000000 < Forcing neutrality... < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < --------------------------------------------------- < APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION < using 5000. points per unit in tabled values < TESTING RELATIVE ERROR over r ranging from 0. to cutoff < --------------------------------------------------- < NSTEP = 5 TIME(PS) = 0.01 TEMP(K) = 295.3 PRESS = 0. < Etot = -8450.139 EKtot = 1866.846 EPtot = -10316.986 < BOND = 28.821 ANGLE = 67.860 DIHED = 69.970 < 1-4 NB = 30.833 1-4 EEL = 509.211 VDWAALS = 1394.843 < EELEC = -12418.527 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 2 EXCHANGE# = 1 < ------------------------------------------------------------------------------ < NSTEP = 10 TIME(PS) = 0.02 TEMP(K) = 289.6 PRESS = 0. < Etot = -8449.503 EKtot = 1830.927 EPtot = -10280.430 < BOND = 23.588 ANGLE = 78.186 DIHED = 75.031 < 1-4 NB = 31.257 1-4 EEL = 514.475 VDWAALS = 1408.903 < EELEC = -12411.872 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 2 EXCHANGE# = 2 < ------------------------------------------------------------------------------ < NSTEP = 15 TIME(PS) = 0.03 TEMP(K) = 285.0 PRESS = 0. < Etot = -8448.757 EKtot = 1801.530 EPtot = -10250.287 < BOND = 26.698 ANGLE = 68.042 DIHED = 77.025 < 1-4 NB = 32.000 1-4 EEL = 519.540 VDWAALS = 1417.791 < EELEC = -12391.386 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 2 EXCHANGE# = 3 < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 0.04 TEMP(K) = 290.5 PRESS = 0. < Etot = -8448.449 EKtot = 1836.550 EPtot = -10285.000 < BOND = 26.125 ANGLE = 70.743 DIHED = 71.357 < 1-4 NB = 29.903 1-4 EEL = 524.563 VDWAALS = 1415.018 < EELEC = -12422.712 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 2 EXCHANGE# = 4 < ------------------------------------------------------------------------------ < NSTEP = 25 TIME(PS) = 0.05 TEMP(K) = 288.3 PRESS = 0. < Etot = -8447.722 EKtot = 1822.649 EPtot = -10270.371 < BOND = 23.883 ANGLE = 67.760 DIHED = 72.804 < 1-4 NB = 33.164 1-4 EEL = 528.453 VDWAALS = 1421.966 < EELEC = -12418.404 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 2 EXCHANGE# = 5 < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 0.06 TEMP(K) = 283.3 PRESS = 0. < Etot = -8446.619 EKtot = 1791.408 EPtot = -10238.028 < BOND = 18.362 ANGLE = 74.966 DIHED = 69.772 < 1-4 NB = 31.429 1-4 EEL = 524.758 VDWAALS = 1439.569 < EELEC = -12396.886 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 2 EXCHANGE# = 6 < ------------------------------------------------------------------------------ < NSTEP = 35 TIME(PS) = 0.07 TEMP(K) = 283.5 PRESS = 0. < Etot = -8445.540 EKtot = 1792.129 EPtot = -10237.670 < BOND = 19.593 ANGLE = 63.241 DIHED = 78.075 < 1-4 NB = 30.830 1-4 EEL = 525.264 VDWAALS = 1433.733 < EELEC = -12388.408 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 2 EXCHANGE# = 7 < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 0.08 TEMP(K) = 292.6 PRESS = 0. < Etot = -8384.570 EKtot = 1850.124 EPtot = -10234.694 < BOND = 28.503 ANGLE = 68.932 DIHED = 77.210 < 1-4 NB = 28.573 1-4 EEL = 524.635 VDWAALS = 1426.699 < EELEC = -12389.247 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 2 EXCHANGE# = 8 < ------------------------------------------------------------------------------ < NSTEP = 45 TIME(PS) = 0.09 TEMP(K) = 290.3 PRESS = 0. < Etot = -8383.275 EKtot = 1835.324 EPtot = -10218.599 < BOND = 25.674 ANGLE = 76.030 DIHED = 70.927 < 1-4 NB = 30.708 1-4 EEL = 519.022 VDWAALS = 1420.227 < EELEC = -12361.191 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 2 EXCHANGE# = 9 < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 289.4 PRESS = 0. < Etot = -8382.113 EKtot = 1829.358 EPtot = -10211.471 < BOND = 25.960 ANGLE = 70.314 DIHED = 73.131 < 1-4 NB = 32.828 1-4 EEL = 519.690 VDWAALS = 1399.660 < EELEC = -12333.058 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 2 EXCHANGE# = 10 < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --------------------------------------- possible FAILURE: check pmd.3.txt.dif /home/makoto/amber12/test/ncsu/premd 1,65d0 < # = NCSU%PMD ================================================================== < # << anchor(1) : position = 7.00000, strength = 3.00000 >> < # ----------------------------------------------------------------------------- < # MD time (ps), CV(1:1) < # ============================================================================= < 0. 6.5186874 < 0.002 6.5188503 < 0.004 6.5194963 < 0.006 6.5204272 < 0.008 6.5214057 < 0.010 6.5222346 < 0.010 6.5222346 < 0.012 6.5228178 < 0.014 6.5231745 < 0.016 6.5234045 < 0.018 6.5236503 < 0.020 6.5240683 < 0.020 6.5240683 < 0.022 6.5247906 < 0.024 6.5258897 < 0.026 6.5273703 < 0.028 6.5291883 < 0.030 6.5312790 < 0.030 6.5312790 < 0.032 6.5335800 < 0.034 6.5360398 < 0.036 6.5386112 < 0.038 6.5412401 < 0.040 6.5438713 < 0.040 6.5438713 < 0.042 6.5464771 < 0.044 6.5490764 < 0.046 6.5517240 < 0.048 6.5544793 < 0.050 6.5573779 < 0.050 6.5573779 < 0.052 6.5604180 < 0.054 6.5635609 < 0.056 6.5667380 < 0.058 6.5698629 < 0.060 6.5728559 < 0.060 6.5728559 < 0.062 6.5756794 < 0.064 6.5783676 < 0.066 6.5810255 < 0.068 6.5837718 < 0.070 6.5866491 < 0.070 6.5866491 < 0.072 6.5895737 < 0.074 6.5923578 < 0.076 6.5947799 < 0.078 6.5966682 < 0.080 6.5979636 < 0.080 6.5979636 < 0.082 6.5987396 < 0.084 6.5991749 < 0.086 6.5994990 < 0.088 6.5999259 < 0.090 6.6005764 < 0.090 6.6005764 < 0.092 6.6014099 < 0.094 6.6022208 < 0.096 6.6027176 < 0.098 6.6026520 < 0.100 6.6019356 --------------------------------------- possible FAILURE: check mdout.3.dif /home/makoto/amber12/test/ncsu/premd 1,166d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < [-O]verwriting output < File Assignments: < Here is the input file: < &cntrl < igb = 0, ntx = 7, irest = 1, < ntb = 1, ntp = 0, temp0 = 320., < ntt = 1, gamma_ln = 0., < ntf = 2, ntc = 2, tol = 0.0000, < cut = 8., dt = 0.00, < ntpr = 5, ntwx = 0, nstlim = 5, < numexchg = 10 < / < ncsu_pmd < output_file = 'pmd.3.txt' < output_freq = 1 < variable ! 1 < type = R_OF_GYRATION < i = (1, 5, 8, 10, 12, 29, 31, 33, 41 < , 43, 53, 55, 57, 59, 70, 72, 74, 84, 86 < , 88, 91, 93, 95, 105, 107, 109, 129, 131, 133 < , 136) < anchor_position = 7. < anchor_strength = 3. < end variable < end ncsu_pmd < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting new box info from bottom of inpcrd < NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 < NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 < NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 < NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 < NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 < IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < BOX TYPE: TRUNCATED OCTAHEDRON < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < NGLY < General flags: < imin = 0, nmropt = 0 < Replica exchange < numexchg= 10, rem= 1 < Nature and format of input: < ntx = 7, irest = 1, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 5, ntrx = 1, ntwr = 500 < iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 < ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 1, igb = 0, nsnb = 25 < ipol = 0, gbsa = 0, iesp = 0 < dielc = 1.0000, cut = 8.0000, intdiel = 1.0000 < Frozen or restrained atoms: < ibelly = 0, ntr = 0 < Molecular dynamics: < nstlim = 5, nscm = 1000, nrespa = 1 < t = 0., dt = 0.0020, vlimit = 20.0000 < Berendsen (weak-coupling) temperature regulation: < temp0 = 320.0000, tempi = 0., tautp = 1.0000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0.0000 < Ewald parameters: < verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 < vdwmeth = 1, eedmeth = 1, netfrc = 1 < Box X = 34.47 Box Y = 34.47 Box Z = 34.47 < Alpha = 109.47 Beta = 109.47 Gamma = 109.47 < NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 < Cutoff= 8.00 Tol =0.10E-4 < Ewald Coefficient = 0.3486 < Interpolation order = 4 < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < NGLY < begin time read from input coords = 0. ps < Number of triangulated 3-point waters found: 1001 < Sum of charges from parm topology file = -0.0000000 < Forcing neutrality... < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < --------------------------------------------------- < APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION < using 5000. points per unit in tabled values < TESTING RELATIVE ERROR over r ranging from 0. to cutoff < --------------------------------------------------- < NSTEP = 5 TIME(PS) = 0.01 TEMP(K) = 309.5 PRESS = 0. < Etot = -8149.415 EKtot = 1956.717 EPtot = -10106.132 < BOND = 27.842 ANGLE = 67.012 DIHED = 74.106 < 1-4 NB = 29.594 1-4 EEL = 526.876 VDWAALS = 1332.725 < EELEC = -12164.290 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 1 < ------------------------------------------------------------------------------ < NSTEP = 10 TIME(PS) = 0.02 TEMP(K) = 303.4 PRESS = 0. < Etot = -8147.565 EKtot = 1918.113 EPtot = -10065.678 < BOND = 33.230 ANGLE = 59.421 DIHED = 77.553 < 1-4 NB = 31.038 1-4 EEL = 525.255 VDWAALS = 1340.946 < EELEC = -12133.125 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 2 < ------------------------------------------------------------------------------ < NSTEP = 15 TIME(PS) = 0.03 TEMP(K) = 307.5 PRESS = 0. < Etot = -8146.949 EKtot = 1943.762 EPtot = -10090.711 < BOND = 34.310 ANGLE = 57.368 DIHED = 76.444 < 1-4 NB = 29.137 1-4 EEL = 521.016 VDWAALS = 1331.279 < EELEC = -12140.268 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 3 < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 0.04 TEMP(K) = 304.2 PRESS = 0. < Etot = -8144.813 EKtot = 1922.994 EPtot = -10067.808 < BOND = 27.684 ANGLE = 62.424 DIHED = 77.477 < 1-4 NB = 31.642 1-4 EEL = 522.489 VDWAALS = 1309.828 < EELEC = -12099.354 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 4 < ------------------------------------------------------------------------------ < NSTEP = 25 TIME(PS) = 0.05 TEMP(K) = 310.2 PRESS = 0. < Etot = -8143.902 EKtot = 1961.287 EPtot = -10105.189 < BOND = 23.002 ANGLE = 68.156 DIHED = 72.990 < 1-4 NB = 30.770 1-4 EEL = 523.261 VDWAALS = 1292.699 < EELEC = -12116.069 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 5 < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 0.06 TEMP(K) = 306.4 PRESS = 0. < Etot = -8141.828 EKtot = 1937.230 EPtot = -10079.058 < BOND = 37.179 ANGLE = 66.370 DIHED = 75.414 < 1-4 NB = 31.422 1-4 EEL = 515.943 VDWAALS = 1277.694 < EELEC = -12083.083 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 6 < ------------------------------------------------------------------------------ < NSTEP = 35 TIME(PS) = 0.07 TEMP(K) = 308.2 PRESS = 0. < Etot = -8141.048 EKtot = 1948.208 EPtot = -10089.256 < BOND = 18.261 ANGLE = 61.435 DIHED = 79.868 < 1-4 NB = 31.570 1-4 EEL = 535.315 VDWAALS = 1258.629 < EELEC = -12074.337 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 7 < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 0.08 TEMP(K) = 311.4 PRESS = 0. < Etot = -8139.820 EKtot = 1968.764 EPtot = -10108.584 < BOND = 24.191 ANGLE = 60.978 DIHED = 76.351 < 1-4 NB = 32.742 1-4 EEL = 533.867 VDWAALS = 1248.822 < EELEC = -12085.538 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 8 < ------------------------------------------------------------------------------ < NSTEP = 45 TIME(PS) = 0.09 TEMP(K) = 309.2 PRESS = 0. < Etot = -8138.276 EKtot = 1954.986 EPtot = -10093.263 < BOND = 33.980 ANGLE = 67.133 DIHED = 71.092 < 1-4 NB = 29.624 1-4 EEL = 529.427 VDWAALS = 1267.757 < EELEC = -12092.279 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 9 < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 307.4 PRESS = 0. < Etot = -8136.680 EKtot = 1943.232 EPtot = -10079.913 < BOND = 27.345 ANGLE = 63.467 DIHED = 76.975 < 1-4 NB = 33.945 1-4 EEL = 541.955 VDWAALS = 1312.173 < EELEC = -12135.774 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 330.000 REPNUM = 3 EXCHANGE# = 10 < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- --------------------------------------- possible FAILURE: check pmd.4.txt.dif /home/makoto/amber12/test/ncsu/premd 1,65d0 < # = NCSU%PMD ================================================================== < # << anchor(1) : position = 8.00000, strength = 4.00000 >> < # ----------------------------------------------------------------------------- < # MD time (ps), CV(1:1) < # ============================================================================= < 0. 8.0143490 < 0.002 8.0166340 < 0.004 8.0192104 < 0.006 8.0221999 < 0.008 8.0255746 < 0.010 8.0291763 < 0.010 8.0291763 < 0.012 8.0327931 < 0.014 8.0362619 < 0.016 8.0395553 < 0.018 8.0428114 < 0.020 8.0462694 < 0.020 8.0462694 < 0.022 8.0501327 < 0.024 8.0544418 < 0.026 8.0590450 < 0.028 8.0636775 < 0.030 8.0680823 < 0.030 8.0680823 < 0.032 8.0720964 < 0.034 8.0756769 < 0.036 8.0788760 < 0.038 8.0817795 < 0.040 8.0844371 < 0.040 8.0844371 < 0.042 8.0868279 < 0.044 8.0888763 < 0.046 8.0905076 < 0.048 8.0917184 < 0.050 8.0926362 < 0.050 8.0926362 < 0.052 8.0935209 < 0.054 8.0946790 < 0.056 8.0963359 < 0.058 8.0985411 < 0.060 8.1011335 < 0.060 8.1011335 < 0.062 8.1037695 < 0.064 8.1060343 < 0.066 8.1076256 < 0.068 8.1085160 < 0.070 8.1089795 < 0.070 8.1089795 < 0.072 8.1094624 < 0.074 8.1103908 < 0.076 8.1120225 < 0.078 8.1143790 < 0.080 8.1172349 < 0.080 8.1172349 < 0.082 8.1201673 < 0.084 8.1226817 < 0.086 8.1243880 < 0.088 8.1251474 < 0.090 8.1251104 < 0.090 8.1251104 < 0.092 8.1246225 < 0.094 8.1240697 < 0.096 8.1237676 < 0.098 8.1239180 < 0.100 8.1245917 --------------------------------------- possible FAILURE: check mdout.4.dif /home/makoto/amber12/test/ncsu/premd 1,166d0 < ------------------------------------------------------- < Amber 12 SANDER 2012 < ------------------------------------------------------- < [-O]verwriting output < File Assignments: < Here is the input file: < &cntrl < igb = 0, ntx = 7, irest = 1, < ntb = 1, ntp = 0, temp0 = 330., < ntt = 1, gamma_ln = 0., < ntf = 2, ntc = 2, tol = 0.0000, < cut = 8., dt = 0.00, < ntpr = 5, ntwx = 0, nstlim = 5, < numexchg = 10 < / < ncsu_pmd < output_file = 'pmd.4.txt' < output_freq = 1 < variable ! 1 < type = R_OF_GYRATION < i = (1, 5, 8, 10, 12, 29, 31, 33, 41 < , 43, 53, 55, 57, 59, 70, 72, 74, 84, 86 < , 88, 91, 93, 95, 105, 107, 109, 129, 131, 133 < , 136) < anchor_position = 8. < anchor_strength = 4. < end variable < end ncsu_pmd < -------------------------------------------------------------------------------- < 1. RESOURCE USE: < -------------------------------------------------------------------------------- < getting new box info from bottom of inpcrd < NATOM = 3143 NTYPES = 15 NBONH = 3064 MBONA = 80 < NTHETH = 139 MTHETA = 110 NPHIH = 283 MPHIA = 199 < NHPARM = 0 NPARM = 0 NNB = 4756 NRES = 1013 < NBONA = 80 NTHETA = 110 NPHIA = 199 NUMBND = 31 < NUMANG = 60 NPTRA = 33 NATYP = 23 NPHB = 1 < IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 < NCOPY = 0 < BOX TYPE: TRUNCATED OCTAHEDRON < -------------------------------------------------------------------------------- < 2. CONTROL DATA FOR THE RUN < -------------------------------------------------------------------------------- < NGLY < General flags: < imin = 0, nmropt = 0 < Replica exchange < numexchg= 10, rem= 1 < Nature and format of input: < ntx = 7, irest = 1, ntrx = 1 < Nature and format of output: < ntxo = 1, ntpr = 5, ntrx = 1, ntwr = 500 < iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 < ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 < Potential function: < ntf = 2, ntb = 1, igb = 0, nsnb = 25 < ipol = 0, gbsa = 0, iesp = 0 < dielc = 1.0000, cut = 8.0000, intdiel = 1.0000 < Frozen or restrained atoms: < ibelly = 0, ntr = 0 < Molecular dynamics: < nstlim = 5, nscm = 1000, nrespa = 1 < t = 0., dt = 0.0020, vlimit = 20.0000 < Berendsen (weak-coupling) temperature regulation: < temp0 = 330.0000, tempi = 0., tautp = 1.0000 < SHAKE: < ntc = 2, jfastw = 0 < tol = 0.0000 < Ewald parameters: < verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 < vdwmeth = 1, eedmeth = 1, netfrc = 1 < Box X = 34.47 Box Y = 34.47 Box Z = 34.47 < Alpha = 109.47 Beta = 109.47 Gamma = 109.47 < NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 < Cutoff= 8.00 Tol =0.10E-4 < Ewald Coefficient = 0.3486 < Interpolation order = 4 < -------------------------------------------------------------------------------- < 3. ATOMIC COORDINATES AND VELOCITIES < -------------------------------------------------------------------------------- < NGLY < begin time read from input coords = 0. ps < Number of triangulated 3-point waters found: 1001 < Sum of charges from parm topology file = -0.0000000 < Forcing neutrality... < -------------------------------------------------------------------------------- < 4. RESULTS < -------------------------------------------------------------------------------- < --------------------------------------------------- < APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION < using 5000. points per unit in tabled values < TESTING RELATIVE ERROR over r ranging from 0. to cutoff < --------------------------------------------------- < NSTEP = 5 TIME(PS) = 0.01 TEMP(K) = 301.8 PRESS = 0. < Etot = -8309.172 EKtot = 1908.125 EPtot = -10217.297 < BOND = 30.151 ANGLE = 54.379 DIHED = 72.348 < 1-4 NB = 28.625 1-4 EEL = 540.268 VDWAALS = 1443.560 < EELEC = -12386.631 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 4 EXCHANGE# = 1 < ------------------------------------------------------------------------------ < NSTEP = 10 TIME(PS) = 0.02 TEMP(K) = 294.8 PRESS = 0. < Etot = -8307.643 EKtot = 1863.860 EPtot = -10171.504 < BOND = 28.748 ANGLE = 67.661 DIHED = 84.685 < 1-4 NB = 29.746 1-4 EEL = 534.623 VDWAALS = 1452.301 < EELEC = -12369.271 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 4 EXCHANGE# = 2 < ------------------------------------------------------------------------------ < NSTEP = 15 TIME(PS) = 0.03 TEMP(K) = 291.9 PRESS = 0. < Etot = -8306.687 EKtot = 1845.443 EPtot = -10152.130 < BOND = 30.461 ANGLE = 64.120 DIHED = 83.435 < 1-4 NB = 28.872 1-4 EEL = 528.457 VDWAALS = 1467.162 < EELEC = -12354.638 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 4 EXCHANGE# = 3 < ------------------------------------------------------------------------------ < NSTEP = 20 TIME(PS) = 0.04 TEMP(K) = 292.6 PRESS = 0. < Etot = -8305.502 EKtot = 1849.859 EPtot = -10155.361 < BOND = 34.171 ANGLE = 70.064 DIHED = 78.503 < 1-4 NB = 30.753 1-4 EEL = 536.651 VDWAALS = 1461.344 < EELEC = -12366.850 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 4 EXCHANGE# = 4 < ------------------------------------------------------------------------------ < NSTEP = 25 TIME(PS) = 0.05 TEMP(K) = 299.1 PRESS = 0. < Etot = -8305.800 EKtot = 1891.038 EPtot = -10196.839 < BOND = 25.126 ANGLE = 59.209 DIHED = 82.505 < 1-4 NB = 32.542 1-4 EEL = 537.015 VDWAALS = 1455.547 < EELEC = -12388.787 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 4 EXCHANGE# = 5 < ------------------------------------------------------------------------------ < NSTEP = 30 TIME(PS) = 0.06 TEMP(K) = 296.5 PRESS = 0. < Etot = -8304.639 EKtot = 1874.734 EPtot = -10179.374 < BOND = 26.696 ANGLE = 57.524 DIHED = 75.829 < 1-4 NB = 34.219 1-4 EEL = 534.228 VDWAALS = 1449.523 < EELEC = -12357.395 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 4 EXCHANGE# = 6 < ------------------------------------------------------------------------------ < NSTEP = 35 TIME(PS) = 0.07 TEMP(K) = 301.3 PRESS = 0. < Etot = -8304.662 EKtot = 1904.712 EPtot = -10209.374 < BOND = 21.541 ANGLE = 62.928 DIHED = 79.072 < 1-4 NB = 33.537 1-4 EEL = 540.424 VDWAALS = 1443.738 < EELEC = -12390.616 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 310.000 REPNUM = 4 EXCHANGE# = 7 < ------------------------------------------------------------------------------ < NSTEP = 40 TIME(PS) = 0.08 TEMP(K) = 288.0 PRESS = 0. < Etot = -8364.743 EKtot = 1820.520 EPtot = -10185.263 < BOND = 29.777 ANGLE = 51.937 DIHED = 80.239 < 1-4 NB = 32.563 1-4 EEL = 541.286 VDWAALS = 1440.965 < EELEC = -12362.031 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 4 EXCHANGE# = 8 < ------------------------------------------------------------------------------ < NSTEP = 45 TIME(PS) = 0.09 TEMP(K) = 293.4 PRESS = 0. < Etot = -8364.759 EKtot = 1854.927 EPtot = -10219.686 < BOND = 27.914 ANGLE = 55.464 DIHED = 77.099 < 1-4 NB = 33.221 1-4 EEL = 543.321 VDWAALS = 1453.462 < EELEC = -12410.170 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 4 EXCHANGE# = 9 < ------------------------------------------------------------------------------ < NSTEP = 50 TIME(PS) = 0.10 TEMP(K) = 286.0 PRESS = 0. < Etot = -8363.141 EKtot = 1808.126 EPtot = -10171.267 < BOND = 32.913 ANGLE = 63.488 DIHED = 76.967 < 1-4 NB = 35.162 1-4 EEL = 540.269 VDWAALS = 1475.630 < EELEC = -12395.698 EHBOND = 0. RESTRAINT = 0. < TEMP0 = 300.000 REPNUM = 4 EXCHANGE# = 10 < ------------------------------------------------------------------------------ < -------------------------------------------------------------------------------- < 5. TIMINGS < -------------------------------------------------------------------------------- ---------------------------------------