------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 07/23/2007 at 20:48:15 [-O]verwriting output File Assignments: | MDIN: step1.in | MDOUT: 1_wat_step1.out |INPCRD: md2.rst | PARM: 1_wat.prmtop |RESTRT: 1_wat_step1.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: 1_wat_step1.mdcrd |MDINFO: 1_wat.mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: step 1 with total 5 steps &cntrl nstlim =3000000, ntx=5, irest=1, ntpr=1000, tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0, ntb=2, pres0=1.0, ntp=1, dt=0.001, ntc=2, ntf=2, ntwr = 10000, ntwx=1000, ntave=1000 icfe=2, clambda=0.0, klambda=4, / -------------------------------------------------------------------------------- 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 = 14.721 | New format PARM file being parsed. | Version = 1.000 Date = 07/23/07 Time = 14:44:57 NATOM = 3551 NTYPES = 6 NBONH = 3545 MBONA = 5 NTHETH = 11 MTHETA = 7 NPHIH = 15 MPHIA = 3 NHPARM = 0 NPARM = 0 NNB = 4767 NRES = 1181 NBONA = 5 NTHETA = 7 NPHIA = 3 NUMBND = 6 NUMANG = 6 NPTRA = 2 NATYP = 6 NPHB = 1 IFBOX = 2 NMXRS = 11 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 269079 | Hollerith 22489 | Integer 100983 | Max Pairs 591833 | nblistReal 42612 | nblist Int 113954 | Total 5674 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- ETN General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 10000 iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 2, 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 Molecular dynamics: nstlim = 3000000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 300.00000, gamma_ln= 5.00000 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 Free energy options: icfe = 2 klambda = 4 clambda = 0.00000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 36.058 Box Y = 36.058 Box Z = 36.058 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 36 NFFT2 = 36 NFFT3 = 36 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- ETN begin time read from input coords = 300.000 ps Number of triangulated 3-point waters found: 1180 | Atom division among processors: | 0 1775 3551 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... | Running AMBER/MPI version on 2 nodes | MULTISANDER: 2 groups. 2 processors out of 4 total. -------------------------------------------------------------------------------- 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 = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 366146 | TOTAL SIZE OF NONBOND LIST = 726282 Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITER, NIT, LL, I and J are : 0 0 5 8 11 Note: This is usually a symptom of some deeper problem with the energetics of the system.