------------------------------------------------------- Amber 16 PMEMD 2016 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 16 | Run on 01/04/2018 at 13:13:52 | Executable path: /lrz/sys/applications/amber/amber16_impi_gen/bin/pmemd.MPI | Working directory: /gpfs/work/pr53wa/di36hoh/300mM_ARG | Hostname: Unknown [-O]verwriting output File Assignments: | MDIN: remd.mdin.001 | MDOUT: 01/remd12.mdout.01 | INPCRD: 01/remd11.rst.01 | PARM: HYA.parm7 | RESTRT: 01/remd12.rst.01 | REFC: refc | MDVEL: mdvel.000 | MDEN: mden.000 | MDCRD: 01/remd12.mdcrd.01 | MDINFO: 01/remd12.mdinfo.01 |LOGFILE: logfile.000 | MDFRC: mdfrc.000 Here is the input file: &cntrl irest=1, ntx=5, nstlim=1000, dt=0.002, ntt=3, gamma_ln=5, temp0=270, ig=-1, ntc=2, ntf=2, ntb=1, ntpr=5000, ntwx=5000, ntwr=100000, nmropt=1, numexchg=2000, iwrap=1, / &wt TYPE='END' / DISANG=HYA_chir.dat Note: ig = -1. Setting random seed to 649678 based on wallclock time in microseconds and disabling the synchronization of random numbers between tasks to improve performance. | Overwriting temp0 from mdin with temp0 from netcdf inpcrd file | Conditional Compilation Defines Used: | MPI | PUBFFT | BINTRAJ | MKL | EMIL | Largest sphere to fit in unit cell has radius = 44.827 | New format PARM file being parsed. | Version = 1.000 Date = 10/06/17 Time = 18:55:30 | 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. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting box info from netcdf restart file NATOM = 89709 NTYPES = 31 NBONH = 85260 MBONA = 4048 NTHETH = 9890 MTHETA = 5215 NPHIH = 18393 MPHIA = 12472 NHPARM = 0 NPARM = 0 NNB = 153702 NRES = 27663 NBONA = 4048 NTHETA = 5215 NPHIA = 12472 NUMBND = 91 NUMANG = 203 NPTRA = 218 NATYP = 54 NPHB = 1 IFBOX = 1 NMXRS = 33 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 17 18 21 | Direct force subcell size = 5.2737 5.0275 5.1243 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 0, nmropt = 1 Replica exchange numexchg= 2000, rem= 1 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 5000, ntrx = 1, ntwr = 100000 iwrap = 1, ntwx = 5000, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 1, igb = 0, 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 = 1000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 649678 temp0 = 270.00000, tempi = 0.00000, gamma_ln= 5.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 5000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 89.654 Box Y = 90.495 Box Z = 107.610 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 90 NFFT2 = 96 NFFT3 = 108 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 | PMEMD ewald parallel performance parameters: | block_fft = 1 | fft_blk_y_divisor = 4 | excl_recip = 1 | excl_master = 1 | atm_redist_freq = 32 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords =104700.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: ** No weight changes given ** RESTRAINTS: Requested file redirections: DISANG = HYA_chir.dat Restraints will be read from file: HYA_chir.dat Here are comments from the DISANG input file: # # trans-omega constraint for residue 5 Number of restraints read = 280 Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 26906 Sum of charges from parm topology file = 0.00009741 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 3451171 | Integers 3223943 | Nonbonded Pairs Initial Allocation: 365242 | Running AMBER/MPI version on 112 MPI task -------------------------------------------------------------------------------- 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 = 0.3316E-14 at 2.351880 | CHECK d/dx switch(x): max rel err = 0.8336E-11 at 2.782960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.47 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.89 |--------------------------------------------------- NSTEP = 5000 TIME(PS) = 104710.000 TEMP(K) = 270.62 PRESS = 0.0 Etot = -292362.2693 EKtot = 49439.8155 EPtot = -341802.0848 BOND = 2196.6918 ANGLE = 4686.3195 DIHED = 5598.8491 1-4 NB = 1401.6954 1-4 EEL = -21957.2986 VDWAALS = 40196.6519 EELEC = -373933.1432 EHBOND = 0.0000 RESTRAINT = 8.1492 EAMBER (non-restraint) = -341810.2340 Ewald error estimate: 0.1718E-04 TEMP0 = 270.0000 REPNUM = 1 EXCHANGE# = 5 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 8.149 ===============================================================================