------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 10/08/2007 at 22:02:13 [-O]verwriting output File Assignments: | MDIN: wat_nsd_md3.in | MDOUT: wat_nsd_md3.out |INPCRD: wat_nsd_md2.rst | PARM: wat_nsd.prmtop |RESTRT: wat_nsd_md3.rst | REFC: wat_nsd_md2.rst | MDVEL: mdvel | MDEN: mden | MDCRD: wat_nsd_md3.mdcrd |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: nsd 15-mer: 5ps MD with res(100) on nsn &cntrl imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10, ntr = 1, ntc = 2, ntf = 2, tempi = 0.0, temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 5000, dt = 0.001, ntpr = 250, ntwx = 250, ntwr = 10000 / Hold the nsd fixed 100.0 RES 1 16 END END -------------------------------------------------------------------------------- 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 = 27.675 | New format PARM file being parsed. | Version = 1.000 Date = 10/07/07 Time = 19:42:41 NATOM = 20778 NTYPES = 17 NBONH = 20165 MBONA = 657 NTHETH = 875 MTHETA = 968 NPHIH = 1772 MPHIA = 1707 NHPARM = 0 NPARM = 0 NNB = 31696 NRES = 6625 NBONA = 657 NTHETA = 968 NPHIA = 1707 NUMBND = 65 NUMANG = 121 NPTRA = 58 NATYP = 47 NPHB = 1 IFBOX = 2 NMXRS = 500 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 1164648 | Hollerith 131295 | Integer 539694 | Max Pairs 11968128 | nblistReal 249336 | nblist Int 668352 | Total 63029 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 = 250, ntrx = 1, ntwr = 10000 iwrap = 0, ntwx = 250, ntwv = 0, ntwe = 0 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 = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Molecular dynamics: nstlim = 5000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 0.00000, 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 = 67.790 Box Y = 67.790 Box Z = 67.790 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 72 NFFT2 = 72 NFFT3 = 72 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES ----- READING GROUP 1; TITLE: Hold the nsd fixed GROUP 1 HAS HARMONIC CONSTRAINTS 100.00000 GRP 1 RES 1 TO 16 Number of atoms in this group = 979 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 20.000 ps Number of triangulated 3-point waters found: 6595 Sum of charges from parm topology file = 0.00360007 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 = 0.3302E-14 at 2.581700 | CHECK d/dx switch(x): max rel err = 0.8030E-11 at 2.732560 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 6538204 | TOTAL SIZE OF NONBOND LIST = 6538204 NSTEP = 0 TIME(PS) = 20.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -83392.4387 EKtot = 0.0000 EPtot = -83392.4387 BOND = 136.2623 ANGLE = 419.1165 DIHED = 642.5903 1-4 NB = 320.1117 1-4 EEL = -3718.8092 VDWAALS = 13370.1684 EELEC = -94561.8787 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.2577E-03 ------------------------------------------------------------------------------ NSTEP = 250 TIME(PS) = 20.250 TEMP(K) = 103.83 PRESS = 0.0 Etot = -78834.8913 EKtot = 4350.4944 EPtot = -83185.3857 BOND = 124.9339 ANGLE = 418.2759 DIHED = 644.5224 1-4 NB = 318.8669 1-4 EEL = -3704.4483 VDWAALS = 13474.5549 EELEC = -94586.3758 EHBOND = 0.0000 RESTRAINT = 124.2845 EAMBER (non-restraint) = -83309.6702 Ewald error estimate: 0.2209E-03 ------------------------------------------------------------------------------