------------------------------------------------------- Amber 8 SANDER Scripps/UCSF 2004 ------------------------------------------------------- | Run on 04/08/2005 at 14:36:53 [-O]verwriting output File Assignments: | MDIN: NVTTGMDdata-f1-new2-8186.in | MDOUT: NVTTGMDdata-f1-new2-8186.out |INPCRD: ../NVTMD8.rst | PARM: ../ntrc.parm |RESTRT: NVTTGMDdata-f1-new2-8186.rst | REFC: ../ref-pntrc2-final.rst | MDVEL: mdvel | MDEN: mden | MDCRD: NVTTGMDdata-f1-new2-8186.dat |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: #Data collection at 298K &cntrl IMIN = 0,ntx=5,irest=1, ntpr=10, ntwr=500, ntb=1,ntr=0, ntf=2,ntc=2, cut=8.5, nscm = 1000, NSTLIM = 400000, DT = 0.002, NTWX=500, NTWV=500,NTWE=500, TEMP0 = 298.0, TEMPI=298.0, NTT=1, TAUTP=2.0, nmropt=1, itgtmd=1, tgtrmsd=4.345, tgtmdfrc=1.00, tgtrmsmask=":3-122", tgtfitmask=":81-86 & !@H=", &end &wt TYPE='TGTRMSD', istep1 =0, istep2 = 200000, value1 = 4.345, value2 = 0.3, &end &wt TYPE='TGTRMSD', istep1 =200001, istep2 = 400000, value1 = 0.3, value2 = 0., &end &wt type="END", &end &rst iat(1)=0, &end END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 24.383 | New format PARM file being parsed. | Version = 1.000 Date = 05/11/04 Time = 13:47:55 NATOM = 16419 NTYPES = 17 NBONH = 15456 MBONA = 974 NTHETH = 2179 MTHETA = 1325 NPHIH = 4033 MPHIA = 2476 NHPARM = 0 NPARM = 0 NNB = 29899 NRES = 4964 NBONA = 974 NTHETA = 1325 NPHIA = 2476 NUMBND = 45 NUMANG = 91 NPTRA = 40 NATYP = 32 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 1226108 | Hollerith 103480 | Integer 1117705 | Max Pairs 6335681 | Max Rstack 932238 | Max Istack 82095 | Total 46701 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 10, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 500, ntwv = 500, ntwe = 500 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 = 1.00000, cut = 8.50000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 400000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 298.00000, tempi = 298.00000, tautp = 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 Targeted molecular dynamics: tgtrmsd = 4.34500, tgtmdfrc= 1.00000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 59.725 Box Y = 59.725 Box Z = 59.725 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 60 NFFT2 = 60 NFFT3 = 60 Cutoff= 8.500 Tol =0.100E-04 Ewald Coefficient = 0.32692 Interpolation order = 4 LOADING THE TARGETED MD ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES Mask ":81-86 & !@H=" matches 44 atoms Mask ":3-122" matches 1844 atoms -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 360.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: TGTRMSD 0 200000 4.345000 0.300000 0 0 TGTRMSD 200001 400000 0.300000 0.000000 0 0 RESTRAINTS: No valid redirection requests found ** No restraint defined ** Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 4833 Sum of charges from parm topology file = -0.00000008 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 0.0 to cutoff | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 3955885 | TOTAL SIZE OF NONBOND LIST = 3955885 NSTEP = 10 TIME(PS) = 360.020 TEMP(K) = 355.07 PRESS = 0.0 Etot = 50500.3752 EKtot = 11923.7546 EPtot = 38576.6206 BOND = 346.8263 ANGLE = 987.1127 DIHED = 1189.6780 1-4 NB = 485.3643 1-4 EEL = 5256.5550 VDWAALS = 5689.6013 EELEC = -64209.2727 EHBOND = 0.0000 RESTRAINT = 88830.7558 EAMBER (non-restraint) = -50254.1352 Ewald error estimate: 0.4247E-04 Current RMSD from reference: 14.160 Current target RMSD: 4.345 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 20 TIME(PS) = 360.040 TEMP(K) = 513.04 PRESS = 0.0 Etot = 49794.4326 EKtot = 17228.8291 EPtot = 32565.6035 BOND = 360.2052 ANGLE = 996.3310 DIHED = 1175.6930 1-4 NB = 566.4743 1-4 EEL = 5333.5054 VDWAALS = 5881.2507 EELEC = -64152.7900 EHBOND = 0.0000 RESTRAINT = 82404.9339 EAMBER (non-restraint) = -49839.3305 Ewald error estimate: 0.5287E-04 Current RMSD from reference: 13.799 Current target RMSD: 4.345 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 30 TIME(PS) = 360.060 TEMP(K) = 733.56 PRESS = 0.0 Etot = 49568.1573 EKtot = 24634.1062 EPtot = 24934.0511 BOND = 433.7839 ANGLE = 1100.1413 DIHED = 1211.9403 1-4 NB = 681.9878 1-4 EEL = 5418.3869 VDWAALS = 6474.5780 EELEC = -64128.7313 EHBOND = 0.0000 RESTRAINT = 73741.9641 EAMBER (non-restraint) = -48807.9131 Ewald error estimate: 0.1075E-03 Current RMSD from reference: 13.288 Current target RMSD: 4.344 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 40 TIME(PS) = 360.080 TEMP(K) = 985.39 PRESS = 0.0 Etot = 50738.3463 EKtot = 33091.0901 EPtot = 17647.2562 BOND = 509.7100 ANGLE = 1351.2235 DIHED = 1288.5195 1-4 NB = 786.7035 1-4 EEL = 5432.4635 VDWAALS = 7447.8058 EELEC = -64042.5993 EHBOND = 0.0000 RESTRAINT = 64873.4298 EAMBER (non-restraint) = -47226.1736 Ewald error estimate: 0.1783E-03 Current RMSD from reference: 12.732 Current target RMSD: 4.344 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 50 TIME(PS) = 360.100 TEMP(K) = 1267.52 PRESS = 0.0 Etot = 53721.7960 EKtot = 42565.3549 EPtot = 11156.4411 BOND = 563.8761 ANGLE = 1601.7784 DIHED = 1412.4925 1-4 NB = 824.8131 1-4 EEL = 5477.7329 VDWAALS = 8342.6842 EELEC = -64000.0255 EHBOND = 0.0000 RESTRAINT = 56933.0894 EAMBER (non-restraint) = -45776.6483 Ewald error estimate: 0.8878E-04 Current RMSD from reference: 12.202 Current target RMSD: 4.344 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 60 TIME(PS) = 360.120 TEMP(K) = 1560.11 PRESS = 0.0 Etot = 57067.4661 EKtot = 52390.8133 EPtot = 4676.6528 BOND = 681.2052 ANGLE = 1932.4337 DIHED = 1575.3324 1-4 NB = 879.3654 1-4 EEL = 5487.3101 VDWAALS = 8810.9370 EELEC = -63642.5994 EHBOND = 0.0000 RESTRAINT = 48952.6684 EAMBER (non-restraint) = -44276.0156 Ewald error estimate: 0.6832E-04 Current RMSD from reference: 11.630 Current target RMSD: 4.344 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 70 TIME(PS) = 360.140 TEMP(K) = 1841.89 PRESS = 0.0 Etot = 60565.8429 EKtot = 61853.5428 EPtot = -1287.6999 BOND = 708.4722 ANGLE = 2331.4137 DIHED = 1774.3048 1-4 NB = 958.5900 1-4 EEL = 5515.1071 VDWAALS = 9612.3293 EELEC = -63380.1996 EHBOND = 0.0000 RESTRAINT = 41192.2826 EAMBER (non-restraint) = -42479.9825 Ewald error estimate: 0.7494E-04 Current RMSD from reference: 11.028 Current target RMSD: 4.344 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 80 TIME(PS) = 360.160 TEMP(K) = 2123.51 PRESS = 0.0 Etot = 63443.4594 EKtot = 71310.7022 EPtot = -7867.2428 BOND = 843.3182 ANGLE = 2794.2482 DIHED = 1801.5359 1-4 NB = 1012.3003 1-4 EEL = 5375.9983 VDWAALS = 9907.3753 EELEC = -62895.9791 EHBOND = 0.0000 RESTRAINT = 33293.9601 EAMBER (non-restraint) = -41161.2029 Ewald error estimate: 0.1824E-03 Current RMSD from reference: 10.353 Current target RMSD: 4.343 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 90 TIME(PS) = 360.180 TEMP(K) = 2372.33 PRESS = 0.0 Etot = 66114.2544 EKtot = 79666.6235 EPtot = -13552.3691 BOND = 869.8000 ANGLE = 3308.4719 DIHED = 1954.7919 1-4 NB = 993.1820 1-4 EEL = 5253.8136 VDWAALS = 10605.0434 EELEC = -62737.9688 EHBOND = 0.0000 RESTRAINT = 26200.4969 EAMBER (non-restraint) = -39752.8660 Ewald error estimate: 0.1640E-03 Current RMSD from reference: 9.674 Current target RMSD: 4.343 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 100 TIME(PS) = 360.200 TEMP(K) = 2590.63 PRESS = 0.0 Etot = 69428.3759 EKtot = 86997.3026 EPtot = -17568.9267 BOND = 979.3832 ANGLE = 3623.9207 DIHED = 2086.0821 1-4 NB = 899.4468 1-4 EEL = 5075.9477 VDWAALS = 11098.2017 EELEC = -62235.3361 EHBOND = 0.0000 RESTRAINT = 20903.4272 EAMBER (non-restraint) = -38472.3539 Ewald error estimate: 0.1686E-03 Current RMSD from reference: 9.104 Current target RMSD: 4.343 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 110 TIME(PS) = 360.220 TEMP(K) = 2778.98 PRESS = 0.0 Etot = 73334.1524 EKtot = 93322.6000 EPtot = -19988.4477 BOND = 1104.6016 ANGLE = 3787.9171 DIHED = 2094.1585 1-4 NB = 915.1784 1-4 EEL = 5008.0793 VDWAALS = 11633.5499 EELEC = -61807.7074 EHBOND = 0.0000 RESTRAINT = 17275.7749 EAMBER (non-restraint) = -37264.2226 Ewald error estimate: 0.2759E-03 Current RMSD from reference: 8.671 Current target RMSD: 4.343 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== vlimit exceeded for step 119 ; vmax = 28.1889953257862 Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITER, NIT, LL, I and J are : 0 2 274 553 554 Note: This is usually a symptom of some deeper problem with the energetics of the system.