------------------------------------------------------- Amber 24 SANDER 2024 ------------------------------------------------------- | Run on 08/09/2025 at 14:54:52 | Executable path: /home/srabani/Downloads/amber24/bin/sander | Working directory: /home/srabani/dulal/FINDGREP | Hostname: srabanigpu2 [-O]verwriting output File Assignments: | MDIN: cp_ph.in.temporary | MDOUT: prod.log |INPCRD: nvt.ncrst | PARM: tyr.prmtop |RESTRT: prod.ncrst | REFC: refc | MDVEL: mdvel | MDFRC: mdfrc | MDEN: mden | MDCRD: prod.nc |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj Here is the input file: Production &cntrl imin=0, ntx=1, irest=0, iwrap=1, nstlim=5000, dt=0.001, temp0=300.0, ntpr=5000, ntwx=5000, cut=10.0, ntb=1, ntp=0, ntt=3, gamma_ln=2.0, icnstph=2, solvph=9.6, ntcnstph=500, ntrelax=200, saltcon=0.1, ig=-1, / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: getting box info from netcdf restart file | NetCDF restart box info found |Largest sphere to fit in unit cell has radius = 17.811 | New format PARM file being parsed. | Version = 1.000 Date = 08/06/25 Time = 14:42:43 NATOM = 5752 NTYPES = 13 NBONH = 5725 MBONA = 17 NTHETH = 33 MTHETA = 22 NPHIH = 65 MPHIA = 40 NHPARM = 0 NPARM = 0 NNB = 7782 NRES = 1916 NBONA = 17 NTHETA = 22 NPHIA = 40 NUMBND = 19 NUMANG = 31 NPTRA = 21 NATYP = 16 NPHB = 0 IFBOX = 1 NMXRS = 21 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) | Memory Use Allocated | Real 1011401 | Hollerith 19174 | Integer 161453 | Max Pairs 3313152 | nblistReal 69024 | nblist Int 198616 | Total 22864 kbytes | 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 BOX TYPE: RECTILINEAR Note: ig = -1. Setting random seed to 492623 based on wallclock time in microseconds. -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- ACE 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 = 5000, ntrx = 1, ntwr = 5000 iwrap = 1, ntwx = 5000, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 1, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 10.00000, intdiel = 1.00000 saltcon = 0.10000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.00000, gbgamma = 0.00000, surften = 0.00500 rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 5000, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 492623 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000 Constant pH options: icnstph = 2 ntcnstph = 500 solvph = 9.60000 ntrelax = 200 mccycles = 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 40.431 Box Y = 38.848 Box Z = 35.621 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 40 NFFT2 = 40 NFFT3 = 36 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 |reading charge increments from file: tyr.cpin.temporary | Attempting 1 MC protonation changes every 500 steps. | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- ACE begin time read from input coords = 2300.000 ps Number of triangulated 3-point waters found: 1903 Sum of charges from parm topology file = 0.00000000 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- | # of SOLUTE degrees of freedom (RNDFP): 17256. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 17256. NUM_NOSHAKE = 0 CORRECTED RNDFP = 17256. | TOTAL # of degrees of freedom (RNDF) = 17256. --------------------------------------------------- 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 = 0.8314E-11 at 2.736960 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 2132299 | TOTAL SIZE OF NONBOND LIST = 2132299 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -19385.2183 EKtot = 0.0000 EPtot = -19385.2183 BOND = 3602.9056 ANGLE = 9.5467 DIHED = 12.2424 1-4 NB = 7.0314 1-4 EEL = 32.9629 VDWAALS = 4117.7224 EELEC = -27167.6297 EHBOND = 0.0000 RESTRAINT = 0.0000 Ewald error estimate: 0.1027E-03 ------------------------------------------------------------------------------ vlimit exceeded for step 30; vmax = 20.2674 vlimit exceeded for step 31; vmax = 20.6280 vlimit exceeded for step 32; vmax = 20.6948 vlimit exceeded for step 33; vmax = 20.7813 vlimit exceeded for step 34; vmax = 20.6423 vlimit exceeded for step 35; vmax = 20.6412 vlimit exceeded for step 36; vmax = 20.6115 vlimit exceeded for step 37; vmax = 20.6294 vlimit exceeded for step 38; vmax = 20.7285 vlimit exceeded for step 39; vmax = 20.7215 vlimit exceeded for step 40; vmax = 20.6946 vlimit exceeded for step 41; vmax = 20.6546 vlimit exceeded for step 42; vmax = 20.6433 vlimit exceeded for step 43; vmax = 20.6673 vlimit exceeded for step 44; vmax = 20.6540 vlimit exceeded for step 45; vmax = 20.7173 vlimit exceeded for step 46; vmax = 20.6826 vlimit exceeded for step 47; vmax = 20.6457 vlimit exceeded for step 48; vmax = 20.6992 vlimit exceeded for step 49; vmax = 20.6086 vlimit exceeded for step 50; vmax = 20.6315 vlimit exceeded for step 51; vmax = 20.6186 vlimit exceeded for step 52; vmax = 20.6328 vlimit exceeded for step 53; vmax = 20.6608 vlimit exceeded for step 54; vmax = 20.6637 vlimit exceeded for step 55; vmax = 20.7195 vlimit exceeded for step 56; vmax = 20.6224 vlimit exceeded for step 57; vmax = 20.7133 vlimit exceeded for step 58; vmax = 20.6966 vlimit exceeded for step 59; vmax = 20.6477 vlimit exceeded for step 60; vmax = 20.7389 vlimit exceeded for step 61; vmax = 20.6262 vlimit exceeded for step 62; vmax = 20.7156 vlimit exceeded for step 63; vmax = 20.6860 vlimit exceeded for step 64; vmax = 20.6633 vlimit exceeded for step 65; vmax = 20.6736 vlimit exceeded for step 66; vmax = 20.6372 vlimit exceeded for step 67; vmax = 20.6268 vlimit exceeded for step 68; vmax = 20.6228 vlimit exceeded for step 69; vmax = 20.7148 vlimit exceeded for step 70; vmax = 20.6056 vlimit exceeded for step 71; vmax = 20.6210 vlimit exceeded for step 72; vmax = 20.6404 vlimit exceeded for step 73; vmax = 20.6404 vlimit exceeded for step 74; vmax = 20.6422 vlimit exceeded for step 75; vmax = 20.6543 vlimit exceeded for step 76; vmax = 20.7433 vlimit exceeded for step 77; vmax = 20.6423 vlimit exceeded for step 78; vmax = 20.5964 vlimit exceeded for step 79; vmax = 20.7199 vlimit exceeded for step 80; vmax = 20.6680 vlimit exceeded for step 81; vmax = 20.6245 vlimit exceeded for step 82; vmax = 20.6401 vlimit exceeded for step 83; vmax = 20.6165 vlimit exceeded for step 84; vmax = 20.6304 vlimit exceeded for step 85; vmax = 20.5971 vlimit exceeded for step 86; vmax = 20.6681 vlimit exceeded for step 87; vmax = 20.6563 vlimit exceeded for step 88; vmax = 20.6952 vlimit exceeded for step 89; vmax = 20.6633 vlimit exceeded for step 90; vmax = 20.5682 vlimit exceeded for step 91; vmax = 20.6496 vlimit exceeded for step 92; vmax = 20.6086 vlimit exceeded for step 93; vmax = 20.6408 vlimit exceeded for step 94; vmax = 20.7751 vlimit exceeded for step 95; vmax = 20.6011 vlimit exceeded for step 96; vmax = 20.7106 vlimit exceeded for step 97; vmax = 20.6505 vlimit exceeded for step 98; vmax = 20.7039 vlimit exceeded for step 99; vmax = 20.6059 vlimit exceeded for step 100; vmax = 20.6972 vlimit exceeded for step 101; vmax = 20.7474 vlimit exceeded for step 102; vmax = 20.6136 vlimit exceeded for step 103; vmax = 20.6697 vlimit exceeded for step 104; vmax = 20.7236 vlimit exceeded for step 105; vmax = 20.6406 vlimit exceeded for step 106; vmax = 20.6255 vlimit exceeded for step 107; vmax = 20.6483 vlimit exceeded for step 108; vmax = 20.6052 vlimit exceeded for step 109; vmax = 20.6234 vlimit exceeded for step 110; vmax = 20.6545 vlimit exceeded for step 111; vmax = 20.6745 vlimit exceeded for step 112; vmax = 20.6427 vlimit exceeded for step 113; vmax = 20.6547 vlimit exceeded for step 114; vmax = 20.6007 vlimit exceeded for step 115; vmax = 20.6604 vlimit exceeded for step 116; vmax = 20.6252 vlimit exceeded for step 117; vmax = 20.6024 vlimit exceeded for step 118; vmax = 20.6205 vlimit exceeded for step 119; vmax = 20.6767 vlimit exceeded for step 120; vmax = 20.6665 vlimit exceeded for step 121; vmax = 20.5865 vlimit exceeded for step 122; vmax = 20.6369 vlimit exceeded for step 123; vmax = 20.6659 vlimit exceeded for step 124; vmax = 20.6939 vlimit exceeded for step 125; vmax = 20.6601 vlimit exceeded for step 126; vmax = 20.6369 vlimit exceeded for step 127; vmax = 20.6357 vlimit exceeded for step 128; vmax = 20.7161 vlimit exceeded for step 129; vmax = 20.6807 vlimit exceeded for step 130; vmax = 20.6562 vlimit exceeded for step 131; vmax = 20.6601 vlimit exceeded for step 132; vmax = 20.6927 vlimit exceeded for step 133; vmax = 20.6789 vlimit exceeded for step 134; vmax = 20.6196 vlimit exceeded for step 135; vmax = 20.6170 vlimit exceeded for step 136; vmax = 20.7301 vlimit exceeded for step 137; vmax = 20.6181 vlimit exceeded for step 138; vmax = 20.6071 vlimit exceeded for step 139; vmax = 20.6559 vlimit exceeded for step 140; vmax = 20.6611 vlimit exceeded for step 141; vmax = 20.7178 vlimit exceeded for step 142; vmax = 20.6842 vlimit exceeded for step 143; vmax = 20.6399 vlimit exceeded for step 144; vmax = 20.5856 vlimit exceeded for step 145; vmax = 20.6393 vlimit exceeded for step 146; vmax = 20.6144 vlimit exceeded for step 147; vmax = 20.6273 vlimit exceeded for step 148; vmax = 20.6497 vlimit exceeded for step 149; vmax = 20.5649 vlimit exceeded for step 150; vmax = 20.6765 vlimit exceeded for step 151; vmax = 20.6503 vlimit exceeded for step 152; vmax = 20.6309 vlimit exceeded for step 153; vmax = 20.7577 vlimit exceeded for step 154; vmax = 20.6823 vlimit exceeded for step 155; vmax = 20.6539 vlimit exceeded for step 156; vmax = 20.6283 vlimit exceeded for step 157; vmax = 20.6598 vlimit exceeded for step 158; vmax = 20.5858 vlimit exceeded for step 159; vmax = 20.6123 vlimit exceeded for step 160; vmax = 20.6849 vlimit exceeded for step 161; vmax = 20.6741 vlimit exceeded for step 162; vmax = 20.6859 vlimit exceeded for step 163; vmax = 20.6585 vlimit exceeded for step 164; vmax = 20.6773 vlimit exceeded for step 165; vmax = 20.6525 vlimit exceeded for step 166; vmax = 20.6615 vlimit exceeded for step 167; vmax = 20.6767 vlimit exceeded for step 168; vmax = 20.6838 vlimit exceeded for step 169; vmax = 20.6488 vlimit exceeded for step 170; vmax = 20.6911 vlimit exceeded for step 171; vmax = 20.6504 vlimit exceeded for step 172; vmax = 20.6732 vlimit exceeded for step 173; vmax = 20.6484 vlimit exceeded for step 174; vmax = 20.6094 vlimit exceeded for step 175; vmax = 20.6656 vlimit exceeded for step 176; vmax = 20.6334 vlimit exceeded for step 177; vmax = 20.6492 vlimit exceeded for step 178; vmax = 20.6416 vlimit exceeded for step 179; vmax = 20.6535 vlimit exceeded for step 180; vmax = 20.6735 vlimit exceeded for step 181; vmax = 20.6024 vlimit exceeded for step 182; vmax = 20.6630 vlimit exceeded for step 183; vmax = 20.6327 vlimit exceeded for step 184; vmax = 20.6588 vlimit exceeded for step 185; vmax = 20.6132 vlimit exceeded for step 186; vmax = 20.6765 vlimit exceeded for step 187; vmax = 20.5755 vlimit exceeded for step 188; vmax = 20.6950 vlimit exceeded for step 189; vmax = 20.7083 vlimit exceeded for step 190; vmax = 20.6444 vlimit exceeded for step 191; vmax = 20.5981 vlimit exceeded for step 192; vmax = 20.6811 vlimit exceeded for step 193; vmax = 20.6667 vlimit exceeded for step 194; vmax = 20.6387 vlimit exceeded for step 195; vmax = 20.6214 vlimit exceeded for step 196; vmax = 20.7095 vlimit exceeded for step 197; vmax = 20.6491 vlimit exceeded for step 198; vmax = 20.6995 vlimit exceeded for step 199; vmax = 20.6881