------------------------------------------------------- Amber 10 SANDER 2008 ------------------------------------------------------- | Run on 12/04/2011 at 13:05:17 [-O]verwriting output File Assignments: | MDIN: heat.in | MDOUT: heat.out |INPCRD: min2.restrt | PARM: test_solvated.prmtop |RESTRT: heat.restrt | REFC: min2.restrt | MDVEL: mdvel | MDEN: mden | MDCRD: heat.x |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | Here is the input file: heat/dynamics at constant volume &cntrl imin=0, ntxo=1, ntrx=1, cut=10.0,tempi=0.1, ntpr=500, ntwx=500, ntwe=500, nstlim=1000, temp0=50.0, dt=0.0005, ntc=1, ntf=1, tol=0.00001, ntx=1, irest=0, ntb=1,tautp=1, ntt=1, nmropt=1,ntr=1 / &wt type='TEMP0', istep1=0, istep2=1000, value1=0.0, value2=50.0, / &wt type='TEMP0', istep1=1001,istep2=80000,value1=50.0, value2=50.0, / &wt type='END', / GROUP FOR CONSTRAINTS 1.0 RES 1 44 END END -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI USE_MPI_IN_PLACE 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 = 16.542 | New format PARM file being parsed. | Version = 1.000 Date = 12/04/11 Time = 12:53:24 NATOM = 6638 NTYPES = 8 NBONH = 5864 MBONA = 602 NTHETH = 1204 MTHETA = 602 NPHIH = 1806 MPHIA = 516 NHPARM = 0 NPARM = 0 NNB = 12090 NRES = 1840 NBONA = 602 NTHETA = 602 NPHIA = 516 NUMBND = 12 NUMANG = 15 NPTRA = 5 NATYP = 11 NPHB = 1 IFBOX = 1 NMXRS = 16 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 448424 | Hollerith 41670 | Integer 214532 | Max Pairs 477936 | nblistReal 79656 | nblist Int 280485 | Total 8089 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- Molecule General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 500, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 500, ntwv = 0, ntwe = 500 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 = 10.00000, intdiel = 1.00000 scnb = 2.00000, scee = 1.20000 Frozen or restrained atoms: ibelly = 0, ntr = 1 Molecular dynamics: nstlim = 1000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00050, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 50.00000, tempi = 0.10000, tautp = 1.00000 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 65.599 Box Y = 33.083 Box Z = 61.086 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 72 NFFT2 = 36 NFFT3 = 64 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 | MPI Timing options: | profile_mpi = 0 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES Mole ----- READING GROUP 1; TITLE: GROUP FOR CONSTRAINTS GROUP 1 HAS HARMONIC CONSTRAINTS 1.00000 GRP 1 RES 1 TO 44 Number of atoms in this group = 704 ----- END OF GROUP READ ----- -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- Mole begin time read from input coords = 0.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: TEMP0 0 1000 0.000000 50.000000 0 0 TEMP0 1001 80000 50.000000 50.000000 0 0 RESTRAINTS: No valid redirection requests found ** No restraint defined ** Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 1754 | Atom division among processors: | 0 832 1658 2489 3317 4145 4976 5804 | 6638 Sum of charges from parm topology file = -0.00000019 Forcing neutrality... | Running AMBER/MPI version on 8 nodes -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- | # of SOLUTE degrees of freedom (RNDFP): 19914. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 19911. NUM_NOSHAKE = 0 CORRECTED RNDFP = 19911. | TOTAL # of degrees of freedom (RNDF) = 19911. --------------------------------------------------- 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 = 154835 | TOTAL SIZE OF NONBOND LIST = 1213915 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.08 PRESS = 0.0 Etot = -24595.8239 EKtot = 1.6037 EPtot = -24597.4277 BOND = 1159.7390 ANGLE = 347.8474 DIHED = 8.7994 1-4 NB = 62.9808 1-4 EEL = 1823.4813 VDWAALS = 2887.0723 EELEC = -30887.3478 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.6408E-04 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== NSTEP = 500 TIME(PS) = 0.250 TEMP(K) = 84.92 PRESS = 0.0 Etot = -25397.0666 EKtot = 1680.0005 EPtot = -27077.0671 BOND = 1385.5428 ANGLE = 357.7905 DIHED = 31.8680 1-4 NB = 68.5052 1-4 EEL = 1848.8314 VDWAALS = 4127.9746 EELEC = -34954.7399 EHBOND = 0.0000 RESTRAINT = 57.1604 EAMBER (non-restraint) = -27134.2274 Ewald error estimate: 0.9287E-04 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== check COM velocity, temp: 0.014583 0.20(Removed) NSTEP = 1000 TIME(PS) = 0.500 TEMP(K) = 106.99 PRESS = 0.0 Etot = -25737.9131 EKtot = 2116.6021 EPtot = -27854.5152 BOND = 1440.2393 ANGLE = 332.6828 DIHED = 67.3166 1-4 NB = 70.8664 1-4 EEL = 1849.1340 VDWAALS = 4389.2354 EELEC = -36130.3880 EHBOND = 0.0000 RESTRAINT = 126.3984 EAMBER (non-restraint) = -27980.9136 Ewald error estimate: 0.4114E-04 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== A V E R A G E S O V E R 1000 S T E P S NSTEP = 1000 TIME(PS) = 0.500 TEMP(K) = 77.23 PRESS = 0.0 Etot = -25345.4540 EKtot = 1527.8802 EPtot = -26873.3342 BOND = 1348.2806 ANGLE = 324.9982 DIHED = 30.1445 1-4 NB = 74.9840 1-4 EEL = 1841.6869 VDWAALS = 4171.5329 EELEC = -34722.6624 EHBOND = 0.0000 RESTRAINT = 57.7012 EAMBER (non-restraint) = -26931.0354 Ewald error estimate: 0.6747E-04 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== R M S F L U C T U A T I O N S NSTEP = 1000 TIME(PS) = 0.500 TEMP(K) = 26.33 PRESS = 0.0 Etot = 278.2714 EKtot = 520.8869 EPtot = 793.3836 BOND = 104.1040 ANGLE = 31.7958 DIHED = 18.3178 1-4 NB = 6.8053 1-4 EEL = 16.9451 VDWAALS = 404.1193 EELEC = 1324.3036 EHBOND = 0.0000 RESTRAINT = 42.4298 EAMBER (non-restraint) = 750.9538 Ewald error estimate: 0.4848E-04 ------------------------------------------------------------------------------ NMR restraints on final step: -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> | Read coords time 0.00 ( 0.01% of Total) | Build the list 0.30 (57.25% of List ) | Other 0.22 (42.75% of List ) | List time 0.52 ( 2.81% of Nonbo) | Short_ene time 8.04 (90.77% of Direc) | Other 0.82 ( 9.23% of Direc) | Direct Ewald time 8.86 (49.75% of Ewald) | Adjust Ewald time 0.15 ( 0.86% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) | Fill Bspline coeffs 0.44 ( 6.63% of Recip) | Fill charge grid 0.47 ( 7.10% of Recip) | Scalar sum 0.95 (14.27% of Recip) | Grad sum 0.50 ( 7.54% of Recip) | FFT back comm time 2.28 (54.32% of FFT t) | Other 1.92 (45.68% of FFT t) | FFT time 4.19 (62.78% of Recip) | Other 0.11 ( 1.68% of Recip) | Recip Ewald time 6.68 (37.51% of Ewald) | Force Adjust 1.67 ( 9.39% of Ewald) | Virial junk 0.38 ( 2.11% of Ewald) | Start sycnronization 0.00 ( 0.01% of Ewald) | Other 0.07 ( 0.38% of Ewald) | Ewald time 17.81 (97.18% of Nonbo) | Other 0.00 ( 0.01% of Nonbo) | Nonbond force 18.32 (93.44% of Force) | Bond/Angle/Dihedral 0.26 ( 1.31% of Force) | FRC Collect time 0.86 ( 4.36% of Force) | Other 0.17 ( 0.89% of Force) | Force time 19.61 (95.62% of Runmd) | Verlet update time 0.25 ( 1.20% of Runmd) | CRD distribute time 0.64 ( 3.14% of Runmd) | Other 0.01 ( 0.05% of Runmd) | Runmd Time 20.51 (99.31% of Total) | Other 0.14 ( 0.68% of Total) | Total time 20.65 (100.0% of ALL ) | Number of list builds : 25 | Highest rstack allocated: 96093 | Highest istack allocated: 1521 | Job began at 13:05:17.281 on 12/04/2011 | Setup done at 13:05:17.424 on 12/04/2011 | Run done at 13:05:37.988 on 12/04/2011 | wallclock() was called 53104 times