------------------------------------------------------- Amber 12 SANDER 2012 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 01/13/2012 at 18:08:05 | WARNING: Stack usage limited by a hard resource limit of 67104768 bytes! | If segment violations occur, get your sysadmin to increase the limit. [-O]verwriting output File Assignments: | MDIN: gbin | MDOUT: mdout.trxox.nogbsa | INPCRD: trxox.2.4ns.x | PARM: prmtop | RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo Here is the input file: test of gen. Born, AO parms &cntrl imin=1, maxcyc=5, cut=99.0, igb=2, saltcon=0.2, gbsa=0, ntpr=1, ntx=1, / | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | New format PARM file being parsed. | Version = 1.000 Date = 01/26/02 Time = 14:17:31 | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- NATOM = 1654 NTYPES = 14 NBONH = 832 MBONA = 838 NTHETH = 1911 MTHETA = 1138 NPHIH = 3388 MPHIA = 2014 NHPARM = 0 NPARM = 0 NNB = 9195 NRES = 108 NBONA = 838 NTHETA = 1138 NPHIA = 2014 NUMBND = 42 NUMANG = 91 NPTRA = 34 NATYP = 27 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 -------------------------------------------------------------------------------- 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 = 0, igb = 2, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 99.00000, intdiel = 1.00000 saltcon = 0.20000, offset = 0.09000, gbalpha= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Energy minimization: maxcyc = 5, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 2405.000 ps Number of triangulated 3-point waters found: 0 | Dynamic Memory, Types Used: | Reals 45406 | Integers 148301 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 -2.3388E+03 2.2094E+01 1.2182E+02 CA 1102 BOND = 631.8993 ANGLE = 898.2543 DIHED = 566.4453 VDWAALS = -768.3629 EEL = -7874.4913 EGB = -2121.8591 1-4 VDW = 348.8246 1-4 EEL = 5980.5047 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 2 -2.3573E+03 2.1772E+01 1.2005E+02 CA 1102 BOND = 618.5484 ANGLE = 893.6994 DIHED = 566.0196 VDWAALS = -768.4675 EEL = -7874.5949 EGB = -2121.7381 1-4 VDW = 348.6933 1-4 EEL = 5980.5144 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 3 -2.3792E+03 2.1388E+01 1.1793E+02 CA 1102 BOND = 602.8397 ANGLE = 888.2823 DIHED = 565.5072 VDWAALS = -768.5935 EEL = -7874.7186 EGB = -2121.5943 1-4 VDW = 348.5364 1-4 EEL = 5980.5259 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 4 -2.4050E+03 2.0931E+01 1.1539E+02 CA 1102 BOND = 584.4360 ANGLE = 881.8510 DIHED = 564.8900 VDWAALS = -768.7455 EEL = -7874.8662 EGB = -2121.4239 1-4 VDW = 348.3488 1-4 EEL = 5980.5395 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 5 -2.4351E+03 2.0388E+01 1.1235E+02 CA 1102 BOND = 562.9902 ANGLE = 874.2312 DIHED = 564.1458 VDWAALS = -768.9292 EEL = -7875.0420 EGB = -2121.2224 1-4 VDW = 348.1247 1-4 EEL = 5980.5555 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 5 -2.4351E+03 2.0388E+01 1.1235E+02 CA 1102 BOND = 562.9902 ANGLE = 874.2312 DIHED = 564.1458 VDWAALS = -768.9292 EEL = -7875.0420 EGB = -2121.2224 1-4 VDW = 348.1247 1-4 EEL = 5980.5555 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 1.59 98.57 | Bond 0.00 0.01 | Angle 0.00 0.17 | Dihedral 0.01 0.53 | Shake 0.00 0.00 | Other 0.01 0.72 | ------------------------------ | Total 1.62 | Generalized Born CPU Time: | | Routine Sec % | ------------------------------------ | Radii Calc 0.28 17.43 | Diagonal Calc 0.55 34.10 | Off Diagonal Calc 0.76 46.96 | GBSA LCPO Calc 0.00 0.00 | --------------------------------- | Total 1.59 98.49 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 1 steps: | Elapsed(s) = 1.63 Per Step(ms) = 1634.97 | ns/day = 0.05 seconds/ns = 1634968.02 | | Average timings for all steps: | Elapsed(s) = 1.63 Per Step(ms) = 1634.97 | ns/day = 0.05 seconds/ns = 1634968.02 | ----------------------------------------------------- | Setup CPU time: 0.04 seconds | NonSetup CPU time: 1.62 seconds | Total CPU time: 1.65 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 2 seconds | Total wall time: 2 seconds 0.00 hours