------------------------------------------------------- Amber 21 SANDER 2021 ------------------------------------------------------- | Run on 09/26/2021 at 23:11:25 | Executable path: /home/ali/amber20_src/cmake-build-debug/AmberTools/src/sander/sander | Working directory: /home/ali/ongoing_research/2_umbrella_amber/2_three_run/1_120_deg | Hostname: Unknown [-O]verwriting output File Assignments: | MDIN: 3_prod.in | MDOUT: 3_prod.out |INPCRD: 2_equil.rst | PARM: ala_tri.prmtop |RESTRT: 3_prod.rst | REFC: refc | MDVEL: mdvel | MDFRC: mdfrc | MDEN: mden | MDCRD: 3_prod.nc |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj Here is the input file: 100 ps NPT production for 120 deg &cntrl imin = 0, ntx = 5, irest = 1, ntpr = 10000, ntwr = 0, ntwx = 10, ntf = 2, ntc = 2, cut = 8.0, ntb = 2, nstlim = 10, dt = 0.001, temp0 = 300.0, ntt = 3, gamma_ln = 1, ntp = 1, pres0 = 1.0, taup = 5.0, nmropt = 1, ioutfm = 1,iwrap=1 / &wt type='DUMPFREQ', istep1=1 / &wt type='END' / DUMPAVE=3_dihedral_120.dat DISANG=1_disang.120 -------------------------------------------------------------------------------- 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 = 13.314 | New format PARM file being parsed. | Version = 1.000 Date = 09/22/21 Time = 23:25:53 NATOM = 3552 NTYPES = 10 NBONH = 2657 MBONA = 894 NTHETH = 36 MTHETA = 18 NPHIH = 64 MPHIA = 45 NHPARM = 0 NPARM = 0 NNB = 6312 NRES = 884 NBONA = 894 NTHETA = 18 NPHIA = 45 NUMBND = 14 NUMANG = 21 NPTRA = 14 NATYP = 11 NPHB = 0 IFBOX = 2 NMXRS = 10 IFCAP = 0 NEXTRA = 880 NCOPY = 0 | CMAP information read from topology file: | Memory Use Allocated | Real 826495 | Hollerith 11542 | Integer 121238 | Max Pairs 1420800 | nblistReal 42624 | nblist Int 118983 | Total 13323 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 |CMAP: Reticulating splines. BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- ACE General flags: imin = 0, nmropt = 1 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 10000, ntrx = 1, ntwr = 10 iwrap = 1, ntwx = 10, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 2, 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 = 10, nscm = 1000, nrespa = 1 t = 0.00000, dt = 0.00100, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 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 Extra-points options: frameon = 1, chngmask= 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 32.613 Box Y = 32.613 Box Z = 32.613 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 32 NFFT2 = 32 NFFT3 = 32 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 2657 0 | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 2657 0 | EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 894 0 | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 14 0 | EXTRA_PTS, trim_theta: num angle BEFORE trim = 36 0 | EXTRA_PTS, trim_theta: num angle AFTER trim = 36 0 | EXTRA_PTS, trim_theta: num angle BEFORE trim = 18 0 | EXTRA_PTS, trim_theta: num angle AFTER trim = 18 0 | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 64 0 | EXTRA_PTS, trim_phi: num diheds AFTER trim = 64 0 | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 45 0 | EXTRA_PTS, trim_phi: num diheds AFTER trim = 45 0 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- ACE begin time read from input coords = 50.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: DUMPFREQ 1 0 0.000000 0.000000 0 0 ** No weight changes given ** RESTRAINTS: Requested file redirections: DUMPAVE = 3_dihedral_120.dat DISANG = 1_disang.120 Restraints will be read from file: 1_disang.120 Here are comments from the DISANG input file: Number of restraints read = 1 Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 880 Sum of charges from parm topology file = 0.00000483 Forcing neutrality... -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- | # of SOLUTE degrees of freedom (RNDFP): 7999. | # of SOLVENT degrees of freedom (RNDFS): 0. | NDFMIN = 7999. NUM_NOSHAKE = 0 CORRECTED RNDFP = 7999. | TOTAL # of degrees of freedom (RNDF) = 7999. --------------------------------------------------- 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 --------------------------------------------------- | Local SIZE OF NONBOND LIST = 981586 | TOTAL SIZE OF NONBOND LIST = 981586 wrapping first mol.: 21.74210 -15.37399 26.62853 wrapping first mol.: 21.74210 -15.37399 26.62853 A V E R A G E S O V E R 10 S T E P S NSTEP = 10 TIME(PS) = 50.010 TEMP(K) = 297.90 PRESS = -183.1 Etot = -9185.0665 EKtot = 1586.2383 EPtot = -10771.3048 BOND = 5.6792 ANGLE = 11.4669 DIHED = 13.9503 1-4 NB = 3.8153 1-4 EEL = 120.7990 VDWAALS = 1509.4665 EELEC = -12438.8499 EHBOND = 0.0000 RESTRAINT = 0.2798 EAMBER (non-restraint) = -10771.5847 EKCMT = 786.9875 VIRIAL = 892.5479 VOLUME = 26703.0496 CMAP = 2.0882 Density = 0.9993 Ewald error estimate: 0.1683E-03 ------------------------------------------------------------------------------ NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.195 =============================================================================== R M S F L U C T U A T I O N S NSTEP = 10 TIME(PS) = 50.010 TEMP(K) = 0.49 PRESS = 44.7 Etot = 4.6398 EKtot = 2.5962 EPtot = 6.9190 BOND = 2.5478 ANGLE = 1.2376 DIHED = 0.3206 1-4 NB = 0.1327 1-4 EEL = 0.3261 VDWAALS = 6.9572 EELEC = 1.7178 EHBOND = 0.0000 RESTRAINT = 0.0939 EAMBER (non-restraint) = 6.8251 EKCMT = 1.2934 VIRIAL = 26.9737 VOLUME = 0.1198 CMAP = 0.0188 Density = 0.0000 Ewald error estimate: 0.1402E-03 ------------------------------------------------------------------------------ NMR restraints on final step: -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | Read coords time 0.02 ( 3.60% of Total) | Fast Water setup 0.00 ( 0.01% of Total) | Build the list 0.04 (88.07% of List ) | Other 0.01 (11.93% of List ) | List time 0.04 (16.73% of Nonbo) | Short_ene time 0.19 (99.23% of Direc) | Other 0.00 ( 0.77% of Direc) | Direct Ewald time 0.19 (83.82% of Ewald) | Adjust Ewald time 0.00 ( 0.69% of Ewald) | Self Ewald time 0.00 ( 0.01% of Ewald) | Fill Bspline coeffs 0.00 ( 5.81% of Recip) | Fill charge grid 0.00 (12.42% of Recip) | Scalar sum 0.01 (25.36% of Recip) | Grad sum 0.01 (25.43% of Recip) | FFT time 0.01 (30.95% of Recip) | Other 0.00 ( 0.04% of Recip) | Recip Ewald time 0.03 (14.85% of Ewald) | Force Adjust 0.00 ( 0.03% of Ewald) | Virial junk 0.00 ( 0.06% of Ewald) | Other 0.00 ( 0.53% of Ewald) | Ewald time 0.22 (83.26% of Nonbo) | Nonbond force 0.27 (93.97% of Force) | Bond/Angle/Dihedral 0.00 ( 0.12% of Force) | Other 0.02 ( 5.91% of Force) | Force time 0.28 (66.28% of Runmd) | Shake time 0.00 ( 0.27% of Runmd) | Verlet update time 0.14 (31.55% of Runmd) | Ekcmr time 0.00 ( 0.03% of Runmd) | Other 0.01 ( 1.86% of Runmd) | Runmd Time 0.43 (79.77% of Total) | Other 0.09 (16.63% of Total) | Total time 0.54 (100.0% of ALL ) | Number of list builds : 1 | Highest rstack allocated: 173302 | Highest istack allocated: 3552 | Final Performance Info: | ----------------------------------------------------- | Average timings for all steps: | Elapsed(s) = 0.44 Per Step(ms) = 43.57 | ns/day = 1.98 seconds/ns = 43574.39 | ----------------------------------------------------- | Job began at 23:11:25.605 on 09/26/2021 | Setup done at 23:11:25.714 on 09/26/2021 | Run done at 23:11:26.143 on 09/26/2021 | wallclock() was called 475 times |3D-RISM memory allocation summary |Type Maximum Current |Integer 0.00000 GB 0.00000 GB |Real 0.00000 GB 0.00000 GB |Logical 0.00000 GB 0.00000 GB |Character 0.00000 GB 0.00000 GB |--------------------------------------- |Total 0.00000 GB 0.00000 GB