------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 05/29/2007 at 14:21:42 [-O]verwriting output File Assignments: | MDIN: a_min.in | MDOUT: a_min_water.out |INPCRD: a.crd | PARM: a.parm7 |RESTRT: a_min.rst | REFC: a.crd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Minimization with Cartesian restraints for the solute &cntrl imin=1, maxcyc=200, ntpr=5, ntr=1, &end Group input for restrained atoms 100.0 RES 1 273 END END -------------------------------------------------------------------------------- 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 = 36.719 | New format PARM file being parsed. | Version = 1.000 Date = 05/29/07 Time = 14:09:10 NATOM = 38710 NTYPES = 21 NBONH = 36607 MBONA = 2115 NTHETH = 4757 MTHETA = 2857 NPHIH = 8930 MPHIA = 6100 NHPARM = 0 NPARM = 0 NNB = 68984 NRES = 11794 NBONA = 2115 NTHETA = 2857 NPHIA = 6100 NUMBND = 54 NUMANG = 108 NPTRA = 65 NATYP = 39 NPHB = 1 IFBOX = 1 NMXRS = 43 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 2679296 | Hollerith 244056 | Integer 1157013 | Max Pairs 12903333 | nblistReal 464520 | nblist Int 2099469 | Total 88638 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 = 5, ntrx = 1, ntwr = 500 iwrap = 0, 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 = 1 Energy minimization: maxcyc = 200, ncyc = 10, 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 = 73.439 Box Y = 77.891 Box Z = 84.139 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 80 NFFT2 = 80 NFFT3 = 90 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Group input for restrained atoms GROUP 1 HAS HARMONIC CONSTRAINTS 100.00000 GRP 1 RES 1 TO 273 Number of atoms in this group = 4133 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 11507 | Atom division among processors: | 0 38710 Sum of charges from parm topology file = -0.00000030 Forcing neutrality... | Running AMBER/MPI version on 1 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 = 0.2738E-14 at 2.422500 | CHECK d/dx switch(x): max rel err = 0.8304E-11 at 2.782960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 6698629 | TOTAL SIZE OF NONBOND LIST = 6698629 NSTEP ENERGY RMS GMAX NAME NUMBER 1 1.1843E+11 2.4284E+10 5.5481E+12 HE3 2239 BOND = 156.1910 ANGLE = 724.2956 DIHED = 2575.2795 VDWAALS = ************* EEL = -129550.8405 HBOND = 0.0000 1-4 VDW = 1223.8779 1-4 EEL = 11866.6783 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 5 2.0734E+10 3.6765E+09 8.3997E+11 HE3 2239 BOND = 156.2236 ANGLE = 724.3259 DIHED = 2575.2803 VDWAALS = ************* EEL = -129551.2666 HBOND = 0.0000 1-4 VDW = 1223.8823 1-4 EEL = 11866.6808 RESTRAINT = 0.0720 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 10 4.0578E+08 5.1538E+07 1.1775E+10 HE3 2239 BOND = 156.6534 ANGLE = 724.7524 DIHED = 2575.2913 VDWAALS = ************* EEL = -129551.9842 HBOND = 0.0000 1-4 VDW = 1223.8969 1-4 EEL = 11866.6887 RESTRAINT = 1.0815 EAMBER = ************* NSTEP ENERGY RMS GMAX NAME NUMBER 15 2.8045E+07 2.6272E+06 5.9935E+08 HE3 2239 BOND = 157.4382 ANGLE = 725.6062 DIHED = 2575.3133 VDWAALS = 28158485.5496 EEL = -129552.2822 HBOND = 0.0000 1-4 VDW = 1223.9139 1-4 EEL = 11866.6977 RESTRAINT = 3.0616 EAMBER = 28045482.2366