------------------------------------------------------- Amber 11 SANDER 2010 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 11 | Run on 12/15/2011 at 18:04:51 [-O]verwriting output File Assignments: | MDIN: mdrun.in | MDOUT: MutChang_MD.out | INPCRD: MutChangVMin.rst | PARM: MutChang.parm7 | RESTRT: MutChang_MD.rst | REFC: MutChangVMin.rst | MDVEL: mdvel | MDEN: mden | MDCRD: MutChang_MD.mdcrd | MDINFO: mdinfo |LOGFILE: logfile Here is the input file: # Protein in water box; simulation at 298K, NPT ntb=2 ntp=1; &cntrl imin=0, ntx=1, ntpr=25000, ntwx=25000, ntwe=25000, ntwprt=0, ntf=2, ntb=2, cut=12.0, ntp=1, pres0=1.0, comp=44.6, taup=1.0, iwrap=1, nscm=250, nstlim=50000000, dt=0.002, ntt=3, temp0=298.0, tautp=1.0, gamma_ln=3, ntc=2, / |--------------------- INFORMATION ---------------------- | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE. | Version 2.1 | | 12/20/2010 | | | Implementation by: | Ross C. Walker (SDSC) | Scott Le Grand (nVIDIA) | Duncan Poole (nVIDIA) | | CAUTION: The CUDA code is currently experimental. | You use it at your own risk. Be sure to | check ALL results carefully. | | Precision model in use: | [SPDP] - Hybrid Single/Double Precision (Default). | |-------------------------------------------------------- |------------------- GPU DEVICE INFO -------------------- | | Task ID: 0 | CUDA Capable Devices Detected: 2 | CUDA Device ID in use: 0 | CUDA Device Name: Tesla M2050 | CUDA Device Global Mem Size: 2687 MB | CUDA Device Num Multiprocessors: 14 | CUDA Device Core Freq: 1.15 GHz | | | Task ID: 1 | CUDA Capable Devices Detected: 2 | CUDA Device ID in use: 1 | CUDA Device Name: Tesla M2050 | CUDA Device Global Mem Size: 2687 MB | CUDA Device Num Multiprocessors: 14 | CUDA Device Core Freq: 1.15 GHz | |-------------------------------------------------------- | Conditional Compilation Defines Used: | DIRFRC_COMTRANS | DIRFRC_EFS | DIRFRC_NOVEC | MPI | PUBFFT | FFTLOADBAL_2PROC | BINTRAJ | CUDA | Largest sphere to fit in unit cell has radius = 45.000 | New format PARM file being parsed. | Version = 1.000 Date = 12/15/11 Time = 17:52:49 | Note: 1-4 EEL scale factors were NOT found in the topology file. | Using default value of 1.2. | Note: 1-4 VDW scale factors were NOT found in the topology file. | Using default value of 2.0. | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- getting new box info from bottom of inpcrd NATOM = 55555 NTYPES = 19 NBONH = 53944 MBONA = 1612 NTHETH = 3488 MTHETA = 2188 NPHIH = 6705 MPHIA = 5478 NHPARM = 0 NPARM = 0 NNB = 87091 NRES = 17708 NBONA = 1612 NTHETA = 2188 NPHIA = 5478 NUMBND = 49 NUMANG = 101 NPTRA = 47 NATYP = 34 NPHB = 1 IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 12 12 12 | Direct force subcell size = 7.5000 7.5000 7.5000 BOX TYPE: RECTILINEAR -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- General flags: imin = 0, nmropt = 0 Nature and format of input: ntx = 1, irest = 0, ntrx = 1 Nature and format of output: ntxo = 1, ntpr = 25000, ntrx = 1, ntwr = 500 iwrap = 1, ntwx = 25000, ntwv = 0, ntwe = 25000 ioutfm = 0, 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 = 12.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 50000000, nscm = 250, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = -1.00000 Langevin dynamics temperature regulation: ig = 71277 temp0 = 298.00000, tempi = 0.00000, gamma_ln= 3.00000 Pressure regulation: ntp = 1 pres0 = 1.00000, comp = 44.60000, taup = 1.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 25000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 90.000 Box Y = 90.000 Box Z = 90.000 Alpha = 90.000 Beta = 90.000 Gamma = 90.000 NFFT1 = 96 NFFT2 = 96 NFFT3 = 96 Cutoff= 12.000 Tol =0.100E-04 Ewald Coefficient = 0.22664 Interpolation order = 4 | PMEMD ewald parallel performance parameters: | block_fft = 0 | fft_blk_y_divisor = 2 | excl_recip = 0 | excl_master = 0 | atm_redist_freq = 320 -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 17468 Sum of charges from parm topology file = -0.00000006 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 3603470 | Integers 2254429 | Nonbonded Pairs Initial Allocation: 17233161 | GPU memory information: | KB of GPU memory in use: 533810 | KB of CPU memory in use: 49947 | Running AMBER/MPI version on 2 nodes -------------------------------------------------------------------------------- 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 = 0.7967E-11 at 2.716640 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.27 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.78 |---------------------------------------------------