------------------------------------------------------- Amber 16 PMEMD 2016 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 16 | Run on 10/26/2017 at 16:42:29 | Executable path: pmemd | Working directory: /home/Jeyaram/4BH4/Fluorination_O8/21.10.17/MD 10 | Hostname: Unknown [-O]verwriting output File Assignments: | MDIN: eq1.in | MDOUT: eq1.out | INPCRD: min2.rst | PARM: 1.prmtop | RESTRT: eq1.rst | REFC: min2.refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo | MDFRC: mdfrc Here is the input file: Heating up the system equilibration stage 1 &cntrl nstlim=100000, dt=0.002, ntx=1, irest=0, ntpr=1000, ntwr=500, ntwx=500, tempi =0.0, temp0=300.0, ntt=1, tautp=2.0, ig=209858, ntb=1, ntp=0, ntc=2, ntf=2, nrespa=2, ntr=1, / Group input for restrained atoms 100.0 RES 1 5 END END | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | EMIL | Largest sphere to fit in unit cell has radius = 35.252 | New format PARM file being parsed. | Version = 1.000 Date = 10/23/17 Time = 15:26:49 | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting box info from netcdf restart file NATOM = 90138 NTYPES = 19 NBONH = 87541 MBONA = 2659 NTHETH = 5817 MTHETA = 3614 NPHIH = 11809 MPHIA = 11494 NHPARM = 0 NPARM = 0 NNB = 141849 NRES = 28656 NBONA = 2659 NTHETA = 3614 NPHIA = 11494 NUMBND = 78 NUMANG = 178 NPTRA = 197 NATYP = 45 NPHB = 1 IFBOX = 1 NMXRS = 34 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 15 16 45 | Direct force subcell size = 4.7003 4.6444 4.5593 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 1000, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 500, 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 = 0.00000 Molecular dynamics: nstlim = 100000, nscm = 0, nrespa = 2 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 300.00000, tempi = 0.00000, tautp = 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 2 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 70.504 Box Y = 74.310 Box Z = 205.168 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 72 NFFT2 = 75 NFFT3 = 216 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES default_name ----- READING GROUP 1; TITLE: Group input for restrained atoms GROUP 1 HAS HARMONIC CONSTRAINTS 100.00000 GRP 1 RES 1 TO 5 Number of atoms in this group = 76 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 28330 Sum of charges from parm topology file = -0.00000313 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 2742320 | Integers 2517863 | Nonbonded Pairs Initial Allocation: 15055299 -------------------------------------------------------------------------------- 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 = 0.8332E-11 at 2.782960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.47 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.89 |--------------------------------------------------- NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -389192.1055 EKtot = 0.0000 EPtot = -389192.1055 BOND = 183.3830 ANGLE = 758.4640 DIHED = 3793.4299 1-4 NB = 991.7475 1-4 EEL = 14623.8843 VDWAALS = 70303.8704 EELEC = -479846.8846 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1112E-03 ------------------------------------------------------------------------------ NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 139.34 PRESS = 0.0 Etot = -295853.6457 EKtot = 25318.6315 EPtot = -321172.2772 BOND = 251.4717 ANGLE = 1120.5416 DIHED = 4080.8985 1-4 NB = 1151.7767 1-4 EEL = 14724.2734 VDWAALS = 59830.7348 EELEC = -402336.8137 EHBOND = 0.0000 RESTRAINT = 4.8397 EAMBER (non-restraint) = -321177.1169 Ewald error estimate: 0.1334E-03 ------------------------------------------------------------------------------ NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 194.51 PRESS = 0.0 Etot = -272160.8212 EKtot = 35342.1315 EPtot = -307502.9527 BOND = 417.2419 ANGLE = 1437.9233 DIHED = 4169.3290 1-4 NB = 1078.2107 1-4 EEL = 14563.1631 VDWAALS = 46862.8109 EELEC = -376040.0659 EHBOND = 0.0000 RESTRAINT = 8.4344 EAMBER (non-restraint) = -307511.3870 Ewald error estimate: 0.6870E-04 ------------------------------------------------------------------------------ vlimit exceeded for step 2329; vmax = 92.8666 Coordinate resetting cannot be accomplished, deviation is too large iter_cnt, my_bond_idx, i and j are : 4 2544 5127 5128