------------------------------------------------------- Amber 22 PMEMD 2022 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 22 | Compiled date/time: Fri Apr 15 02:06:37 2022 | Run on 12/09/2022 at 20:14:07 | Executable path: pmemd.cuda | Working directory: /smb/zhangxh/AmberTutorial/01 | Hostname: Unknown [-O]verwriting output File Assignments: | MDIN: min.in | MDOUT: min.out | INPCRD: inpcrd | PARM: prmtop | RESTRT: min.rst | REFC: inpcrd | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: mdinfo | MDFRC: mdfrc Here is the input file: Minimize ! type anything you want &cntrl ! this line's called namelist imin=1, ntx=1, irest=0, maxcyc=2000, ntmin=1, ncyc=1000, ntpr=100, ntwx=0, cut=8.0, / Note: ig = -1. Setting random seed to 623529 based on wallclock time in microseconds. | irandom = 1, using AMBER's internal random number generator (default). |--------------------- INFORMATION ---------------------- | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE. | Version 18.0.0 | | 03/25/2018 | | Implementation by: | Ross C. Walker (SDSC) | Scott Le Grand (nVIDIA) | | Version 18 performance extensions by: | David Cerutti (Rutgers) | | Precision model in use: | [SPFP] - Single Precision Forces, 64-bit Fixed Point | Accumulation. (Default) | |-------------------------------------------------------- |----------------- CITATION INFORMATION ----------------- | | When publishing work that utilized the CUDA version | of AMBER, please cite the following in addition to | the regular AMBER citations: | | - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan | Poole; Scott Le Grand; Ross C. Walker "Routine | microsecond molecular dynamics simulations with | AMBER - Part II: Particle Mesh Ewald", J. Chem. | Theory Comput., 2013, 9 (9), pp3878-3888, | DOI: 10.1021/ct400314y. | | - Andreas W. Goetz; Mark J. Williamson; Dong Xu; | Duncan Poole; Scott Le Grand; Ross C. Walker | "Routine microsecond molecular dynamics simulations | with AMBER - Part I: Generalized Born", J. Chem. | Theory Comput., 2012, 8 (5), pp1542-1555. | | - Scott Le Grand; Andreas W. Goetz; Ross C. Walker | "SPFP: Speed without compromise - a mixed precision | model for GPU accelerated molecular dynamics | simulations.", Comp. Phys. Comm., 2013, 184 | pp374-380, DOI: 10.1016/j.cpc.2012.09.022 | |-------------------------------------------------------- |------------------- GPU DEVICE INFO -------------------- | | CUDA_VISIBLE_DEVICES: 0 | CUDA Capable Devices Detected: 1 | CUDA Device ID in use: 0 | CUDA Device Name: NVIDIA GeForce RTX 4090 | CUDA Device Global Mem Size: 24255 MB | CUDA Device Num Multiprocessors: 128 | CUDA Device Core Freq: 2.52 GHz | |-------------------------------------------------------- | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | CUDA | EMIL | Largest sphere to fit in unit cell has radius = 16.635 | New format PARM file being parsed. | Version = 1.000 Date = 12/09/22 Time = 15:53:52 | 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 new box info from bottom of inpcrd NATOM = 4307 NTYPES = 11 NBONH = 4263 MBONA = 43 NTHETH = 117 MTHETA = 55 NPHIH = 202 MPHIA = 166 NHPARM = 0 NPARM = 0 NNB = 6121 NRES = 1411 NBONA = 43 NTHETA = 55 NPHIA = 166 NUMBND = 30 NUMANG = 59 NPTRA = 51 NATYP = 18 NPHB = 0 IFBOX = 1 NMXRS = 22 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 9 10 7 | Direct force subcell size = 4.5693 4.5969 4.7528 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 1, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 100, 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 = 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 Energy minimization: maxcyc = 2000, ncyc = 1000, ntmin = 1 dx0 = 0.01000, drms = 0.00010 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 0 Box X = 41.123 Box Y = 45.969 Box Z = 33.270 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 48 NFFT2 = 48 NFFT3 = 36 Cutoff= 8.000 Tol =0.100E-04 Ewald Coefficient = 0.34864 Interpolation order = 4 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 1404 Sum of charges from parm topology file = -0.00000000 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 227734 | Integers 126066 | Nonbonded Pairs Initial Allocation: 719376 | GPU memory information (estimate): | KB of GPU memory in use: 29144 | KB of CPU memory in use: 23474 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP ENERGY RMS GMAX NAME NUMBER 1 -1.0950E+04 1.9506E+01 4.7913E+02 HG2 83 BOND = 0.4979 ANGLE = 2.0576 DIHED = 16.6056 UB = 0.0000 IMP = 0.0000 CMAP = -2.7488 VDWAALS = 1709.1085 EEL = -13053.5610 HBOND = 0.0000 1-4 VDW = 27.9270 1-4 EEL = 350.4903 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 100 -1.4119E+04 3.7366E+00 2.2877E+02 C 88 BOND = 847.9878 ANGLE = 17.6160 DIHED = 20.8761 UB = 0.0000 IMP = 0.0000 CMAP = -1.5580 VDWAALS = 1495.3888 EEL = -16860.8845 HBOND = 0.0000 1-4 VDW = 15.9316 1-4 EEL = 345.7438 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 200 -1.4691E+04 6.6380E-01 1.6911E+01 C 88 BOND = 890.7740 ANGLE = 8.6384 DIHED = 20.7083 UB = 0.0000 IMP = 0.0000 CMAP = -1.4615 VDWAALS = 1790.1027 EEL = -17762.3035 HBOND = 0.0000 1-4 VDW = 15.6971 1-4 EEL = 346.3743 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 300 -1.5027E+04 1.0435E+00 6.7038E+01 C 88 BOND = 952.3430 ANGLE = 8.2622 DIHED = 20.4713 UB = 0.0000 IMP = 0.0000 CMAP = -1.3435 VDWAALS = 2046.2090 EEL = -18414.3971 HBOND = 0.0000 1-4 VDW = 15.4289 1-4 EEL = 346.0191 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 400 -1.5265E+04 8.8430E-01 5.4989E+01 C 88 BOND = 1001.2397 ANGLE = 8.0628 DIHED = 20.2246 UB = 0.0000 IMP = 0.0000 CMAP = -1.2363 VDWAALS = 2257.4744 EEL = -18911.2782 HBOND = 0.0000 1-4 VDW = 15.3193 1-4 EEL = 345.6299 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 500 -1.5442E+04 4.1547E-01 1.0507E+01 C 88 BOND = 1037.6099 ANGLE = 7.3342 DIHED = 20.1700 UB = 0.0000 IMP = 0.0000 CMAP = -1.1540 VDWAALS = 2423.4278 EEL = -19290.2412 HBOND = 0.0000 1-4 VDW = 15.1710 1-4 EEL = 345.3548 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 600 -1.5583E+04 6.1247E-01 3.4345E+01 C 88 BOND = 1067.6134 ANGLE = 7.2418 DIHED = 20.1167 UB = 0.0000 IMP = 0.0000 CMAP = -1.0811 VDWAALS = 2555.2427 EEL = -19592.6523 HBOND = 0.0000 1-4 VDW = 15.0459 1-4 EEL = 345.0599 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 700 -1.5696E+04 3.3577E-01 7.3392E+00 C 88 BOND = 1090.3478 ANGLE = 6.9124 DIHED = 20.1265 UB = 0.0000 IMP = 0.0000 CMAP = -1.0271 VDWAALS = 2658.0754 EEL = -19829.7180 HBOND = 0.0000 1-4 VDW = 14.9014 1-4 EEL = 344.8546 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 800 -1.5791E+04 1.2786E+00 8.1700E+01 C 88 BOND = 1113.2329 ANGLE = 7.0800 DIHED = 20.1130 UB = 0.0000 IMP = 0.0000 CMAP = -0.9834 VDWAALS = 2747.6016 EEL = -20037.0321 HBOND = 0.0000 1-4 VDW = 14.7502 1-4 EEL = 344.6435 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 900 -1.5877E+04 1.0725E+00 6.4618E+01 C 88 BOND = 1129.6869 ANGLE = 7.0555 DIHED = 19.8898 UB = 0.0000 IMP = 0.0000 CMAP = -0.9348 VDWAALS = 2825.5420 EEL = -20217.1669 HBOND = 0.0000 1-4 VDW = 14.6048 1-4 EEL = 344.2716 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1000 -1.5954E+04 9.1708E-01 5.2718E+01 C 88 BOND = 1144.4996 ANGLE = 6.5883 DIHED = 19.7195 UB = 0.0000 IMP = 0.0000 CMAP = -0.8964 VDWAALS = 2894.8714 EEL = -20377.0112 HBOND = 0.0000 1-4 VDW = 14.3916 1-4 EEL = 343.9205 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1100 -1.6308E+04 1.0646E+00 3.5499E+01 O 3891 BOND = 1230.0555 ANGLE = 6.3106 DIHED = 19.0688 UB = 0.0000 IMP = 0.0000 CMAP = -0.6453 VDWAALS = 3236.3102 EEL = -21154.3390 HBOND = 0.0000 1-4 VDW = 13.6439 1-4 EEL = 341.3473 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1200 -1.6457E+04 6.2261E-01 1.3560E+01 H2 3893 BOND = 1247.5598 ANGLE = 6.8658 DIHED = 18.5012 UB = 0.0000 IMP = 0.0000 CMAP = -0.3994 VDWAALS = 3337.9945 EEL = -21422.2019 HBOND = 0.0000 1-4 VDW = 13.7280 1-4 EEL = 340.6834 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1300 -1.6676E+04 5.8015E-01 1.9366E+01 CD 85 BOND = 1291.3224 ANGLE = 5.2302 DIHED = 17.6803 UB = 0.0000 IMP = 0.0000 CMAP = -0.1732 VDWAALS = 3529.3944 EEL = -21876.1082 HBOND = 0.0000 1-4 VDW = 13.7878 1-4 EEL = 343.0506 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1400 -1.6771E+04 4.0019E-01 1.0305E+01 C 32 BOND = 1311.0968 ANGLE = 5.1842 DIHED = 17.7001 UB = 0.0000 IMP = 0.0000 CMAP = -0.1268 VDWAALS = 3612.1098 EEL = -22074.0590 HBOND = 0.0000 1-4 VDW = 13.8374 1-4 EEL = 343.3359 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1500 -1.6844E+04 5.0482E-01 1.4078E+01 O 3891 BOND = 1326.0869 ANGLE = 5.9337 DIHED = 17.6883 UB = 0.0000 IMP = 0.0000 CMAP = 0.0910 VDWAALS = 3673.4146 EEL = -22224.4796 HBOND = 0.0000 1-4 VDW = 14.0081 1-4 EEL = 343.4105 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1600 -1.6912E+04 2.9516E-01 5.8896E+00 CB 79 BOND = 1340.9260 ANGLE = 4.8885 DIHED = 17.5187 UB = 0.0000 IMP = 0.0000 CMAP = 0.1707 VDWAALS = 3724.7174 EEL = -22357.3348 HBOND = 0.0000 1-4 VDW = 13.7959 1-4 EEL = 343.2911 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1700 -1.6989E+04 4.2479E-01 9.8668E+00 O 3627 BOND = 1358.2618 ANGLE = 4.8203 DIHED = 17.3600 UB = 0.0000 IMP = 0.0000 CMAP = 0.3639 VDWAALS = 3794.3293 EEL = -22521.2662 HBOND = 0.0000 1-4 VDW = 13.8011 1-4 EEL = 342.8623 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1800 -1.7027E+04 4.1787E-01 9.9297E+00 C 5 BOND = 1363.9585 ANGLE = 4.7628 DIHED = 17.2948 UB = 0.0000 IMP = 0.0000 CMAP = 0.4380 VDWAALS = 3816.3240 EEL = -22586.0474 HBOND = 0.0000 1-4 VDW = 13.7817 1-4 EEL = 342.7535 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 1900 -1.7069E+04 4.2741E-01 9.8111E+00 C 32 BOND = 1370.7675 ANGLE = 4.7879 DIHED = 17.2520 UB = 0.0000 IMP = 0.0000 CMAP = 0.4858 VDWAALS = 3835.2549 EEL = -22653.8309 HBOND = 0.0000 1-4 VDW = 13.7972 1-4 EEL = 342.3167 RESTRAINT = 0.0000 NSTEP ENERGY RMS GMAX NAME NUMBER 2000 -1.7109E+04 3.8129E-01 9.0295E+00 CD 85 BOND = 1377.1433 ANGLE = 4.7695 DIHED = 16.9096 UB = 0.0000 IMP = 0.0000 CMAP = 0.5306 VDWAALS = 3852.0928 EEL = -22716.3735 HBOND = 0.0000 1-4 VDW = 13.7774 1-4 EEL = 342.3159 RESTRAINT = 0.0000 Maximum number of minimization cycles reached. FINAL RESULTS NSTEP ENERGY RMS GMAX NAME NUMBER 2000 -1.7109E+04 3.8129E-01 9.0295E+00 CD 85 BOND = 1377.1433 ANGLE = 4.7695 DIHED = 16.9096 UB = 0.0000 IMP = 0.0000 CMAP = 0.5306 VDWAALS = 3852.0928 EEL = -22716.3735 HBOND = 0.0000 1-4 VDW = 13.7774 1-4 EEL = 342.3159 RESTRAINT = 0.0000 -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 0.22 42.50 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.00 0.00 | Shake 0.00 0.00 | Other 0.29 57.50 | ------------------------------ | Total 0.51 | PME Nonbond Pairlist CPU Time: | | Routine Sec % | --------------------------------- | Set Up Cit 0.00 0.00 | Build List 0.00 0.00 | --------------------------------- | Total 0.00 0.00 | PME Direct Force CPU Time: | | Routine Sec % | --------------------------------- | NonBonded Calc 0.00 0.00 | Exclude Masked 0.00 0.00 | Other 0.00 0.33 | --------------------------------- | Total 0.00 0.33 | PME Reciprocal Force CPU Time: | | Routine Sec % | --------------------------------- | 1D bspline 0.00 0.00 | Grid Charges 0.00 0.00 | Scalar Sum 0.00 0.00 | Gradient Sum 0.00 0.00 | FFT 0.00 0.00 | --------------------------------- | Total 0.00 0.00 | Setup CPU time: 0.28 seconds | NonSetup CPU time: 0.51 seconds | Total CPU time: 0.79 seconds 0.00 hours | Setup wall time: 0 seconds | NonSetup wall time: 0 seconds | Total wall time: 0 seconds 0.00 hours