------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- | Run on 11/12/2008 at 21:21:54 [-O]verwriting output File Assignments: | MDIN: min | MDOUT: min.out.p2 |INPCRD: inpcrd | PARM: prmtop2 |RESTRT: min.rst.p2 | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd_02.traj.p2 |MDINFO: mdinfo |INPDIP: inpdip |RSTDIP: rstdip Here is the input file: Initial Minimization of solvent + ions &cntrl imin = 1, maxcyc = 10, ncyc = 5, ntb = 1, ntr = 0, cut = 8.0, ntpr = 1, ntx = 1, icfe=1,klambda=6,clambda=0.5 / -------------------------------------------------------------------------------- 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 = 17.507 | New format PARM file being parsed. | Version = 1.000 Date = 04/25/08 Time = 21:40:08 NATOM = 6017 NTYPES = 18 NBONH = 5923 MBONA = 100 NTHETH = 102 MTHETA = 154 NPHIH = 230 MPHIA = 283 NHPARM = 0 NPARM = 0 NNB = 8592 NRES = 1966 NBONA = 100 NTHETA = 154 NPHIA = 283 NUMBND = 34 NUMANG = 60 NPTRA = 38 NATYP = 27 NPHB = 1 IFBOX = 1 NMXRS = 37 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 470050 | Hollerith 38070 | Integer 166747 | Max Pairs 1002833 | nblistReal 72204 | nblist Int 205002 | Total 9754 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 = 1, 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 = 0 Energy minimization: maxcyc = 10, ncyc = 5, ntmin = 1 dx0 = 0.01000, drms = 0.00010 Free energy options: icfe = 1 klambda = 6 clambda = 0.50000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 42.884 Box Y = 42.884 Box Z = 42.884 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 48 NFFT2 = 45 NFFT3 = 45 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 Setting ifbox to 3 for non-orthogonal unit cell -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 120.000 ps Number of triangulated 3-point waters found: 1959 | Atom division among processors: | 0 3008 6017 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 = 604911 | TOTAL SIZE OF NONBOND LIST = 1240054 NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.9492E+04 1.4590E+01 2.0668E+02 C2 123 BOND = 65.1043 ANGLE = 80.4082 DIHED = 101.1669 VDWAALS = 2744.6319 EEL = -22064.8064 HBOND = 0.0000 1-4 VDW = 34.3886 1-4 EEL = -452.6342 RESTRAINT = 0.0000 DV/DL = 63.6210 NSTEP ENERGY RMS GMAX NAME NUMBER 2 -1.9515E+04 1.4426E+01 2.0284E+02 C2 123 BOND = 63.6621 ANGLE = 80.0455 DIHED = 101.1098 VDWAALS = 2743.1691 EEL = -22084.8087 HBOND = 0.0000 1-4 VDW = 34.3642 1-4 EEL = -452.6629 RESTRAINT = 0.0000 DV/DL = 63.3062 NSTEP ENERGY RMS GMAX NAME NUMBER 3 -1.9543E+04 1.4232E+01 1.9828E+02 C2 123 BOND = 62.2883 ANGLE = 79.6195 DIHED = 101.0413 VDWAALS = 2741.4160 EEL = -22108.8572 HBOND = 0.0000 1-4 VDW = 34.3357 1-4 EEL = -452.6969 RESTRAINT = 0.0000 DV/DL = 62.9319 NSTEP ENERGY RMS GMAX NAME NUMBER 4 -1.9576E+04 1.4002E+01 1.9287E+02 C2 123 BOND = 61.1455 ANGLE = 79.1212 DIHED = 100.9589 VDWAALS = 2739.3182 EEL = -22137.7461 HBOND = 0.0000 1-4 VDW = 34.3025 1-4 EEL = -452.7369 RESTRAINT = 0.0000 DV/DL = 62.4876 NSTEP ENERGY RMS GMAX NAME NUMBER 5 -1.9614E+04 1.3731E+01 1.8648E+02 C2 123 BOND = 60.4885 ANGLE = 78.5413 DIHED = 100.8600 VDWAALS = 2736.7928 EEL = -22172.4310 HBOND = 0.0000 1-4 VDW = 34.2641 1-4 EEL = -452.7838 RESTRAINT = 0.0000 DV/DL = 61.9616 NSTEP ENERGY RMS GMAX NAME NUMBER 6 -1.9660E+04 1.3412E+01 1.7893E+02 C2 123 BOND = 60.7043 ANGLE = 77.8704 DIHED = 100.7410 VDWAALS = 2733.7752 EEL = -22214.1075 HBOND = 0.0000 1-4 VDW = 34.2202 1-4 EEL = -452.8384 RESTRAINT = 0.0000 DV/DL = 61.3409 NSTEP ENERGY RMS GMAX NAME NUMBER 7 -1.9661E+04 1.3405E+01 1.7877E+02 C2 123 BOND = 60.7214 ANGLE = 77.8557 DIHED = 100.7383 VDWAALS = 2733.7082 EEL = -22215.0379 HBOND = 0.0000 1-4 VDW = 34.2192 1-4 EEL = -452.8396 RESTRAINT = 0.0000 DV/DL = 61.3273 NSTEP ENERGY RMS GMAX NAME NUMBER 8 -1.9938E+04 1.1395E+01 1.2921E+02 C2 123 BOND = 89.6429 ANGLE = 74.0643 DIHED = 99.9642 VDWAALS = 2713.7233 EEL = -22496.1513 HBOND = 0.0000 1-4 VDW = 33.9636 1-4 EEL = -453.1981 RESTRAINT = 0.0000 DV/DL = 57.2578 NSTEP ENERGY RMS GMAX NAME NUMBER 9 -2.0605E+04 9.5687E+00 1.3610E+02 C2 123 BOND = 1058.9519 ANGLE = 74.8456 DIHED = 96.8820 VDWAALS = 2613.5313 EEL = -24027.2297 HBOND = 0.0000 1-4 VDW = 33.4844 1-4 EEL = -455.3165 RESTRAINT = 0.0000 DV/DL = 36.1407 NSTEP ENERGY RMS GMAX NAME NUMBER 10 -2.1171E+04 4.1243E+00 3.6642E+01 C4 82 BOND = 1513.0938 ANGLE = 52.1428 DIHED = 94.2203 VDWAALS = 2562.2555 EEL = -24975.1829 HBOND = 0.0000 1-4 VDW = 34.1594 1-4 EEL = -452.0856 RESTRAINT = 0.0000 DV/DL = 44.0139 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 10 -2.1171E+04 4.1243E+00 3.6642E+01 C4 82 BOND = 1513.0938 ANGLE = 52.1428 DIHED = 94.2203 VDWAALS = 2562.2555 EEL = -24975.1829 HBOND = 0.0000 1-4 VDW = 34.1594 1-4 EEL = -452.0856 RESTRAINT = 0.0000 DV/DL = 44.0139 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.02 ( 0.63% of Total) | Fast Water setup 0.00 ( 0.02% of Total) | Build the list 0.08 (59.07% of List ) | Other 0.06 (40.93% of List ) | List time 0.13 (17.97% of Nonbo) | Short_ene time 0.39 (98.04% of Direc) | Other 0.01 ( 1.96% of Direc) | Direct Ewald time 0.39 (63.84% of Ewald) | Adjust Ewald time 0.00 ( 0.68% of Ewald) | Self Ewald time 0.00 ( 0.02% of Ewald) | Fill Bspline coeffs 0.01 ( 4.00% of Recip) | Fill charge grid 0.01 ( 6.95% of Recip) | Scalar sum 0.07 (33.09% of Recip) | Grad sum 0.02 ( 8.92% of Recip) | FFT back comm time 0.02 (22.31% of FFT t) | Other 0.07 (77.69% of FFT t) | FFT time 0.09 (46.72% of Recip) | Other 0.00 ( 0.31% of Recip) | Recip Ewald time 0.20 (31.90% of Ewald) | Force Adjust 0.02 ( 3.34% of Ewald) | Virial junk 0.00 ( 0.21% of Ewald) | Other 0.00 ( 0.01% of Ewald) | Ewald time 0.62 (82.03% of Nonbo) | Nonbond force 0.75 (97.83% of Force) | Bond/Angle/Dihedral 0.00 ( 0.54% of Force) | FRC Collect time 0.01 ( 1.03% of Force) | Other 0.00 ( 0.60% of Force) | Force time 0.77 (100.0% of Runmd) | Runmd Time 0.77 (25.27% of Total) | Other 2.25 (74.08% of Total) | Total time 3.04 (100.0% of ALL ) | Highest rstack allocated: 288051 | Highest istack allocated: 4635 | Job began at 21:21:54.843 on 11/12/2008 | Setup done at 21:21:55.193 on 11/12/2008 | Run done at 21:21:57.882 on 11/12/2008 | wallclock() was called 450 times