------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 03/14/2007 at 17:51:27 [-O]verwriting output File Assignments: | MDIN: /home/eric/MD/mdin/minimization.mdin | MDOUT: /common/eric/MD/mdout/hno3_solution_2.min.mdout |INPCRD: ../crd/hno3_solution_2.crd | PARM: /home/eric/MD/top/hno3_solution_2.top |RESTRT: /common/eric/MD/crd/hno3_solution_2.min.crd | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: General minimization script &cntrl IMIN = 1, IWRAP = 1, NTPR = 250, NTMIN = 1, MAXCYC = 100000, NCYC = 3500, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI 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 = 15.000 | New format PARM file being parsed. | Version = 1.000 Date = 03/14/07 Time = 16:49:13 NATOM = 2670 NTYPES = 6 NBONH = 2154 MBONA = 387 NTHETH = 129 MTHETA = 387 NPHIH = 258 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 4119 NRES = 804 NBONA = 387 NTHETA = 387 NPHIA = 0 NUMBND = 5 NUMANG = 3 NPTRA = 1 NATYP = 6 NPHB = 1 IFBOX = 1 NMXRS = 5 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 252203 | Hollerith 16826 | Integer 85329 | Max Pairs 445000 | nblistReal 32040 | nblist Int 113375 | Total 4800 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 250, ntrx = 1, ntwr = 500 iwrap = 1, ntwx = 0, 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 = 8.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 100000, ncyc = 3500, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 30.000 Box Y = 30.000 Box Z = 30.000 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 30 NFFT2 = 30 NFFT3 = 30 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 675 | Atom division among processors: | 0 1335 2670 Sum of charges from parm topology file = -0.00000021 Forcing neutrality... | Running AMBER/MPI version on 2 nodes -------------------------------------------------------------------------------- 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 = 0.3132E-14 at 2.452700 | CHECK d/dx switch(x): max rel err = 0.8063E-11 at 2.773160 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 264112 | TOTAL SIZE OF NONBOND LIST = 556765 NSTEP ENERGY RMS GMAX NAME NUMBER 1 4.1709E+11 1.5809E+11 7.2311E+12 O 2500 BOND = 356.6873 ANGLE = 51.5459 DIHED = 0.0092 VDWAALS = ************* EEL = 193.2689 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = -6143.6685 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 250 -4.0319E+06 3.9172E+09 1.8545E+11 H 559 BOND = 369.8618 ANGLE = 563.6761 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = -4029233.7698 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -5.1727E+07 6.4765E+11 3.0661E+13 H 559 BOND = 369.8611 ANGLE = 563.6750 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 750 -1.9087E+07 8.8128E+10 4.1721E+12 H 559 BOND = 369.8612 ANGLE = 563.6751 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -4.0319E+06 3.9172E+09 1.8545E+11 H 559 BOND = 369.8618 ANGLE = 563.6761 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = -4029233.7749 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1250 -5.1727E+07 6.4765E+11 3.0661E+13 H 559 BOND = 369.8611 ANGLE = 563.6750 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1500 -1.9087E+07 8.8128E+10 4.1721E+12 H 559 BOND = 369.8612 ANGLE = 563.6751 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1750 -4.0319E+06 3.9172E+09 1.8545E+11 H 559 BOND = 369.8618 ANGLE = 563.6761 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = -4029233.7749 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 2000 -5.1727E+07 6.4765E+11 3.0661E+13 H 559 BOND = 369.8611 ANGLE = 563.6750 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 2250 -1.9087E+07 8.8128E+10 4.1721E+12 H 559 BOND = 369.8612 ANGLE = 563.6751 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 2500 -4.0319E+06 3.9172E+09 1.8545E+11 H 559 BOND = 369.8618 ANGLE = 563.6761 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = -4029233.7749 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 2750 -5.1727E+07 6.4765E+11 3.0661E+13 H 559 BOND = 369.8611 ANGLE = 563.6750 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 3000 -1.9087E+07 8.8128E+10 4.1721E+12 H 559 BOND = 369.8612 ANGLE = 563.6751 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 3250 -4.0319E+06 3.9172E+09 1.8545E+11 H 559 BOND = 369.8618 ANGLE = 563.6761 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = -4029233.7749 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 3500 -5.1727E+07 6.4765E+11 3.0661E+13 H 559 BOND = 369.8611 ANGLE = 563.6750 DIHED = 184.9566 VDWAALS = 1422.5695 EEL = -5191.2051 HBOND = 0.0000 1-4 VDW = 0.0000 1-4 EEL = ************* RESTRAINT = 0.0000