File Assignments: | MDIN: heat.in | MDOUT: heat.out | INPCRD: ../minimization/min.rst | PARM: ../protein_complex.prmtop | RESTRT: heat.rst | REFC: ../minimization/min.rst | MDVEL: mdvel | MDEN: mden | MDCRD: heat.mdcrd | MDINFO: mdinfo | MDFRC: mdfrc Here is the input file: heat protein_complex &cntrl imin=0,irest=0,ntx=1, nstlim=250000,dt=0.002, ntc=2,ntf=2, cut=8.0, ntb=1, ntpr=500, ntwx=500, ntt=3, gamma_ln=2.0, vlimit=20, tempi=0.0, temp0=300.0, ig=-1, ntr=1, restraintmask=':1-359', restraint_wt=2.0, nmropt=1 / &wt TYPE='TEMP0', istep1=0, istep2=25000, value1=0.1, value2=300.0, / &wt TYPE='END' / Note: ig = -1. Setting random seed to 817587 based on wallclock time in microseconds. | irandom = 1, using AMBER's internal random number generator (default). | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | EMIL | Largest sphere to fit in unit cell has radius = 40.509 | New format PARM file being parsed. | Version = 1.000 Date = 08/29/18 Time = 03:30:14 | 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 = 50485 NTYPES = 20 NBONH = 47503 MBONA = 3030 NTHETH = 6835 MTHETA = 4085 NPHIH = 13760 MPHIA = 12673 NHPARM = 0 NPARM = 0 NNB = 92405 NRES = 15219 NBONA = 3030 NTHETA = 4085 NPHIA = 12673 NUMBND = 80 NUMANG = 181 NPTRA = 195 NATYP = 46 NPHB = 1 IFBOX = 1 NMXRS = 58 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 19 18 19 | Direct force subcell size = 4.6935 4.5010 4.5550 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 500, ntrx = 1, ntwr = 250000 iwrap = 0, ntwx = 500, 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 = 1 restraint_wt = 2.00000 Molecular dynamics: nstlim = 250000, nscm = 0, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 817587 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000 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 = 500 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 89.176 Box Y = 81.019 Box Z = 86.545 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 90 NFFT2 = 90 NFFT3 = 90 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES default_name Mask :1-359; matches 5953 atoms -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 0.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: TEMP0 0 25000 0.100000 300.000000 0 0 RESTRAINTS: ** No restraint defined ** Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 14836 Sum of charges from parm topology file = 0.00100079 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 1592828 | Integers 1890904 | Nonbonded Pairs Initial Allocation: 8432257 -------------------------------------------------------------------------------- 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 = 0.8332E-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 = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -140705.5594 EKtot = 0.0000 EPtot = -140705.5594 BOND = 210.8121 ANGLE = 930.5872 DIHED = 4327.3834 1-4 NB = 1243.0829 1-4 EEL = 18362.3910 VDWAALS = 5754.8226 EELEC = -171534.6386 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.7279E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000 =============================================================================== vlimit exceeded for step 100; vmax = 37.9402 vlimit exceeded for step 101; vmax = 93.2563 Coordinate resetting cannot be accomplished, deviation is too large iter_cnt, my_bond_idx, i and j are : 3 2991 5903 5904