------------------------------------------------------- Amber 20 PMEMD 2020 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 18 | Compiled date/time: Mon Apr 27 20:19:54 2020 | Run on 12/11/2021 at 01:43:46 | Executable path: pmemd | Working directory: /home/chemistry/NFS/projects_ali/14_wat_to_oh_mail | Hostname: Unknown [-O]verwriting output File Assignments: | MDIN: oh.in | MDOUT: oh.out | INPCRD: oh.rst7 | PARM: oh.parm7 | RESTRT: oh.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: oh.nc | MDINFO: oh.mdinfo | MDFRC: mdfrc Here is the input file: &cntrl ntb = 0,igb=6, imin = 0, nstlim = 1, dt=0.00, cut = 20.0, ntt = 1, tautp = 1.0, temp0 = 0, tempi = 0 / Note: ig = -1. Setting random seed to 190340 based on wallclock time in microseconds. | irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | EMIL | New format PARM file being parsed. | Version = 1.000 Date = 12/11/21 Time = 01:35:18 | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | INFO: Reading atomic numbers from topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- NATOM = 3 NTYPES = 3 NBONH = 1 MBONA = 0 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0 NHPARM = 0 NPARM = 0 NNB = 3 NRES = 2 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 1 NUMANG = 0 NPTRA = 0 NATYP = 3 NPHB = 1 IFBOX = 1 NMXRS = 2 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are modified Bondi radii (mbondi) BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- tmp General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 50, ntrx = 1, ntwr = 1 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 0, igb = 6, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 20.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 1, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00000, vlimit = 20.00000 Berendsen (weak-coupling) temperature regulation: temp0 = 0.00000, tempi = 0.00000, tautp = 1.00000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 50 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- tmp begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 0 | Dynamic Memory, Types Used: | Reals 83 | Integers 45 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -114.5940 EKtot = 0.0000 EPtot = -114.5940 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = -0.1884 EELEC = -114.4056 EGB = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 0.00 0.38 | Bond 0.00 0.38 | Angle 0.00 0.00 | Dihedral 0.00 0.00 | Shake 0.00 0.00 | RunMD 0.00 98.08 | Other 0.00 1.15 | ------------------------------ | Total 0.00 | Generalized Born CPU Time: | | Routine Sec % | ------------------------------------ | Radii Calc 0.00 0.00 | Diagonal Calc 0.00 0.00 | Off Diagonal Calc 0.00 0.38 | GBSA LCPO Calc 0.00 0.00 | --------------------------------- | Total 0.00 0.38 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 1 steps: | Elapsed(s) = 0.00 Per Step(ms) = 2.80 | ns/day = 0.00 seconds/ns = Infinity | | Average timings for all steps: | Elapsed(s) = 0.00 Per Step(ms) = 2.80 | ns/day = 0.00 seconds/ns = Infinity | ----------------------------------------------------- | Setup CPU time: 0.00 seconds | NonSetup CPU time: 0.00 seconds | Total CPU time: 0.00 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 0 seconds | Total wall time: 0 seconds 0.00 hours