------------------------------------------------------- PBSA VERSION 2009 UC Irvine ------------------------------------------------------- | Run on 09/12/2011 at 14:25:15 [-O]verwriting output File Assignments: | MDIN: pbsa.in | MDOUT: pbsa.out |INPCRD: vac.inpcrd | PARM: vac.prmtop | Here is the input file: &cntrl imin =0, igb=10, / &pb sprob=1.6, radiopt=1 / PB Info in pb_read(): npopt has been overwritten with inp -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 09/04/11 Time = 23:27:11 NATOM = 688 NTYPES = 10 NBONH = 260 MBONA = 476 NTHETH = 536 MTHETA = 672 NPHIH = 1036 MPHIA = 964 NHPARM = 0 NPARM = 0 NNB = 3513 NRES = 45 NBONA = 476 NTHETA = 672 NPHIA = 964 NUMBND = 13 NUMANG = 19 NPTRA = 9 NATYP = 12 NPHB = 0 IFBOX = 0 NMXRS = 17 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated | Real 17385 | Hollerith 4175 | Integer 45378 | Max Pairs 1 | Max Rstack 1 | Max Istack 1 | Total 329 kbytes -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- MOL 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 = 50, 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, ipb = 1, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 1, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- MOL begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- Total surface charge 2.0090 Reaction field energy -545.9633 Cavity solvation energy 319.0811 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -487.0979 EKtot = 0.0000 EPtot = -487.0979 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -133.0002 EELEC = -127.2155 EPB = -545.9633 RESTRAINT = 0.0000 ECAVITY= 319.0811 EDISPER = 0.0000 ------------------------------------------------------------------------------ NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0 Etot = -487.1017 EKtot = 0.0000 EPtot = -487.1017 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -133.0002 EELEC = -127.2155 EPB = -545.9671 RESTRAINT = 0.0000 ECAVITY= 319.0811 EDISPER = 0.0000 ------------------------------------------------------------------------------ A V E R A G E S O V E R 1 S T E P S NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0 Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000 EELEC = 0.0000 EPB = 0.0000 RESTRAINT = 0.0000 ECAVITY= 0.0000 EDISPER = 0.0000 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0 Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000 EELEC = 0.0000 EPB = 0.0000 RESTRAINT = 0.0000 ECAVITY= 0.0000 EDISPER = 0.0000 |E(PBS) = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Total time 12.37 | Read prm/crd time 0.11 | Runmd Time 12.25 | Force time 12.25 | Nonbond force 12.25 | PB Nonbond 11.16 | PB NB list 0.02 | PB FD grid 0.01 | PB Sasa 1.13 | PB FD force 9.96 | PB Set linear sys 2.38 | PB Solver 5.11 | PB Direct 0.05 | NP Nonbond 1.08 | NP Sasa 1.08 | NP Cavity 0.00 | PB SA arc 2.14 | PB SA arc setup 0.02 | PB circle 1.57 | PB exclude 0.54 | PB exmol 2.35 | PB exmol setup 0.05 | PB exmol part a 0.02 | PB exmol part b 0.26 | PB exmol part c 0.08 | PB exmol part d 0.02 | PB exmol part e 0.47 | PB exmol part f 1.34 | PB epsbnd 0.03 | PB epsmap 0.09 | Job began at 14:25:15.551 on 09/12/2011 | Setup done at 14:25:15.669 on 09/12/2011 | Run done at 14:25:27.923 on 09/12/2011 | wallclock() was called 218 times