------------------------------------------------------- Amber 24 PMEMD 2024 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 24 | Compiled date/time: Sat Jun 22 15:57:56 2024 | Run on 08/07/2025 at 11:38:49 | Executable path: /home/srabani/Downloads/amber24/bin/pmemd.cuda | 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 | MDEN: mden | MDCRD: prod.nc | MDINFO: mdinfo | MDFRC: mdfrc 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, / Note: ig = -1. Setting random seed to 223168 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 | | When publishing work that utilized the CUDA version | of Constant pH MD please cite the following in | addition to the regular AMBER GPU citations: | | - Daniel J. Mermelstein; J. Andrew McCammon; Ross C. Walker | "pH dependent conformational dynamics of Beta-secretase 1: | a molecular dynamics study". | J. Chem. Theory Comput., 2018, in review. | | |-------------------------------------------------------- |------------------- GPU DEVICE INFO -------------------- | | CUDA_VISIBLE_DEVICES: not set | CUDA Capable Devices Detected: 1 | CUDA Device ID in use: 0 | CUDA Device Name: Tesla V100-PCIE-32GB | CUDA Device Global Mem Size: 32500 MB | CUDA Device Num Multiprocessors: 80 | CUDA Device Core Freq: 1.38 GHz | |-------------------------------------------------------- | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | CUDA | EMIL | 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 | 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. | INFO: Reading atomic numbers from topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting box info from netcdf restart file 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) |reading charge increments from file: tyr.cpin.temporary | Coordinate Index Table dimensions: 7 7 6 | Direct force subcell size = 5.7759 5.5497 5.9369 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 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= 0.80000 gbbeta = 0.00000, gbgamma = 2.90912, 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 = -1.00000 Langevin dynamics temperature regulation: ig = 223168 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000 Constant pH options: icnstph = 2 ntcnstph = 500 solvph = 9.60000 ntrelax = 200 mccycles = 1 | 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 = 40.431 Box Y = 38.848 Box Z = 35.621 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 48 NFFT2 = 40 NFFT3 = 36 Cutoff= 10.000 Tol =0.100E-04 Ewald Coefficient = 0.27511 Interpolation order = 4 -------------------------------------------------------------------------------- 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... | Dynamic Memory, Types Used: | Reals 345681 | Integers 208511 | Nonbonded Pairs Initial Allocation: 1739836 | GPU memory information (estimate): | KB of GPU memory in use: 44424 | KB of CPU memory in use: 13208 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -19385.2013 EKtot = 0.0000 EPtot = -19385.2013 BOND = 3602.9056 ANGLE = 9.5467 DIHED = 12.2424 1-4 NB = 7.0314 1-4 EEL = 32.9629 VDWAALS = 4117.7233 EELEC = -27167.6136 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ NSTEP = 5000 TIME(PS) = 5.000 TEMP(K) = 299.03 PRESS = 0.0 Etot = -14343.7421 EKtot = 5127.0337 EPtot = -19470.7757 BOND = 3612.2725 ANGLE = 11.4093 DIHED = 14.1180 1-4 NB = 9.6968 1-4 EEL = 25.2673 VDWAALS = 3988.2011 EELEC = -27131.7406 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ A V E R A G E S O V E R 1 S T E P S NSTEP = 5000 TIME(PS) = 5.000 TEMP(K) = 299.03 PRESS = 0.0 Etot = -14343.7421 EKtot = 5127.0337 EPtot = -19470.7757 BOND = 3612.2725 ANGLE = 11.4093 DIHED = 14.1180 1-4 NB = 9.6968 1-4 EEL = 25.2673 VDWAALS = 3988.2011 EELEC = -27131.7406 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ R M S F L U C T U A T I O N S NSTEP = 5000 TIME(PS) = 5.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- | NonSetup CPU Time in Major Routines: | | Routine Sec % | ------------------------------ | Nonbond 4.84 29.95 | Bond 0.00 0.00 | Angle 0.00 0.00 | Dihedral 0.00 0.00 | Shake 0.00 0.00 | RunMD 11.22 69.47 | Other 0.09 0.58 | ------------------------------ | Total 16.14 | 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 0.01 0.03 | --------------------------------- | Total 0.01 0.03 | 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 | Final Performance Info: | ----------------------------------------------------- | Average timings for last 5000 steps: | Elapsed(s) = 16.26 Per Step(ms) = 3.25 | ns/day = 26.56 seconds/ns = 3252.84 | | Average timings for all steps: | Elapsed(s) = 16.26 Per Step(ms) = 3.25 | ns/day = 26.56 seconds/ns = 3252.84 | ----------------------------------------------------- | Setup CPU time: 1.08 seconds | NonSetup CPU time: 16.14 seconds | Total CPU time: 17.23 seconds 0.00 hours | Setup wall time: 3 seconds | NonSetup wall time: 16 seconds | Total wall time: 19 seconds 0.01 hours