------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 06/10/2008 at 17:26:42 [-O]verwriting output File Assignments: | MDIN: eq_sol1_jun.in | MDOUT: eq_sol1_jun.out |INPCRD: 2V0A_pro_ED_sol2_min.rst | PARM: 2V0A_pro_ED_sol.prmtop |RESTRT: 2V0A_pro_ED_eq_sol1_jun.rst | REFC: 2V0A_pro_ED_sol2_min.rst | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Stage 1 - Initial Equilibration/Heating From 150 K to 310 K - Protein Fixed - 4 &cntrl imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10, ntr = 1, ntc = 2, ig = 192456, tempi = 150.0 temp0 = 310.0, ntt = 3, gamma_ln = 1.0, nstlim = 20000, dt = 0.002, ntpr = 100, ntwx = 100, ntwr = 1000, restraint_wt = 5.0, restraintmask=' :1 - 306 ', / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting new box info from bottom of inpcrd | INFO: Old style inpcrd file read | peek_ewald_inpcrd: Box info found |Largest sphere to fit in unit cell has radius = 34.506 | New format PARM file being parsed. | Version = 1.000 Date = 06/05/08 Time = 12:54:58 NATOM = 41250 NTYPES = 17 NBONH = 39021 MBONA = 2256 NTHETH = 4944 MTHETA = 3044 NPHIH = 9421 MPHIA = 7674 NHPARM = 0 NPARM = 0 NNB = 73256 NRES = 12603 NBONA = 2256 NTHETA = 3044 NPHIA = 7674 NUMBND = 45 NUMANG = 94 NPTRA = 42 NATYP = 32 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 2229411 | Hollerith 260105 | Integer 1241417 | Max Pairs 23760000 | nblistReal 495000 | nblist Int 1420696 | Total 125511 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- 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 = 100, ntrx = 1, ntwr = 1000 iwrap = 0, ntwx = 100, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Molecular dynamics: nstlim = 20000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 192456 temp0 = 310.00000, tempi = 150.00000, gamma_ln= 1.00000 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 = 84.521 Box Y = 84.521 Box Z = 84.521 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 90 NFFT2 = 90 NFFT3 = 90 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES Mask :1 - 306; matches 4377 atoms -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 12288 Sum of charges from parm topology file = -0.00000015 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 = 0.8313E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 13262618 | TOTAL SIZE OF NONBOND LIST = 13262618 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 219.42 PRESS = 0.0 Etot = -146157.8742 EKtot = 18472.1678 EPtot = -164630.0421 BOND = 12329.1132 ANGLE = 760.0366 DIHED = 2466.7112 1-4 NB = 842.1355 1-4 EEL = 15234.9510 VDWAALS = 29032.6348 EELEC = -225295.6244 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.3661E-04 ------------------------------------------------------------------------------ NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 121.14 PRESS = 0.0 Etot = -132231.5008 EKtot = 10198.7222 EPtot = -142430.2231 BOND = 427.4136 ANGLE = 1378.6018 DIHED = 2585.4474 1-4 NB = 876.1224 1-4 EEL = 15200.8601 VDWAALS = 19739.9803 EELEC = -182884.6352 EHBOND = 0.0000 RESTRAINT = 245.9864 EAMBER (non-restraint) = -142676.2094 Ewald error estimate: 0.2110E-04 ------------------------------------------------------------------------------ NSTEP = 200 TIME(PS) = 0.400 TEMP(K) = 156.30 PRESS = 0.0 Etot = -126450.6128 EKtot = 13158.6461 EPtot = -139609.2589 BOND = 501.0856 ANGLE = 1542.8283 DIHED = 2606.4005 1-4 NB = 894.7816 1-4 EEL = 15221.9519 VDWAALS = 19837.1994 EELEC = -180533.5313 EHBOND = 0.0000 RESTRAINT = 320.0250 EAMBER (non-restraint) = -139929.2839 Ewald error estimate: 0.8789E-04 ------------------------------------------------------------------------------ NSTEP = 300 TIME(PS) = 0.600 TEMP(K) = 183.84 PRESS = 0.0 Etot = -121819.3309 EKtot = 15477.0211 EPtot = -137296.3520 BOND = 540.9059 ANGLE = 1667.2011 DIHED = 2646.9215 1-4 NB = 908.4025 1-4 EEL = 15256.9238 VDWAALS = 19154.4139 EELEC = -177856.9157 EHBOND = 0.0000 RESTRAINT = 385.7948 EAMBER (non-restraint) = -137682.1469 Ewald error estimate: 0.1033E-03 ------------------------------------------------------------------------------ NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = 206.81 PRESS = 0.0 Etot = -117822.7182 EKtot = 17410.8191 EPtot = -135233.5372 BOND = 637.4520 ANGLE = 1786.6720 DIHED = 2687.0105 1-4 NB = 907.6490 1-4 EEL = 15222.5903 VDWAALS = 18526.8613 EELEC = -175438.1512 EHBOND = 0.0000 RESTRAINT = 436.3788 EAMBER (non-restraint) = -135669.9161 Ewald error estimate: 0.7856E-04 ------------------------------------------------------------------------------ NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 222.84 PRESS = 0.0 Etot = -114656.6972 EKtot = 18759.7006 EPtot = -133416.3978 BOND = 649.8757 ANGLE = 1926.5233 DIHED = 2695.9671 1-4 NB = 926.2299 1-4 EEL = 15233.6904 VDWAALS = 18229.5795 EELEC = -173548.4341 EHBOND = 0.0000 RESTRAINT = 470.1704 EAMBER (non-restraint) = -133886.5682 Ewald error estimate: 0.2841E-04 ------------------------------------------------------------------------------