------------------------------------------------------- Amber 14 SANDER 2014 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 14 | Run on 08/10/2016 at 09:28:17 | Executable path: pmemd.cuda | Working directory: /home/ucl/eisuc270/3SDY/G33E/md | Hostname: cn3g07.gpu.rl.ac.uk [-O]verwriting output File Assignments: | MDIN: min_1.ctl | MDOUT: min_1.out | INPCRD: 3SDY_wat.inpcrd | PARM: 3SDY_wat.prmtop | RESTRT: min_1.rst | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd | MDINFO: min_1.mdinfo | MDFRC: mdfrc Here is the input file: Minimisation &cntrl imin=1, !Minimisation ntx = 1, !Read just co-ordinates maxcyc=4000, ncyc = 2000, !1000 steps SD, 1000 CG ntc=1, ntf=1, !No shake during minimisation ntb=1, ntp=0, !Constant volume ntpr=50, !Print to mdout every 50 steps cut=8.0, !8 Angstrom VDW cutoff / |--------------------- INFORMATION ---------------------- | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE. | Version 14.0 | | 01/31/2014 | | Implementation by: | Ross C. Walker (SDSC) | Scott Le Grand (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: | [SPFP] - Mixed Single/Double/Fixed Point Precision. | (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: not set | CUDA Capable Devices Detected: 3 | CUDA Device ID in use: 0 | CUDA Device Name: Tesla M2090 | CUDA Device Global Mem Size: 5375 MB | CUDA Device Num Multiprocessors: 16 | CUDA Device Core Freq: 1.30 GHz | |-------------------------------------------------------- | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | CUDA | EMIL | Largest sphere to fit in unit cell has radius = 84.408 | New format PARM file being parsed. | Version = 1.000 Date = 08/09/16 Time = 22:11:00 | 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 = 636132 NTYPES = 17 NBONH = 614565 MBONA = 22068 NTHETH = 47433 MTHETA = 30000 NPHIH = 98478 MPHIA = 98340 NHPARM = 0 NPARM = 0 NNB = 1026085 NRES = 200677 NBONA = 22068 NTHETA = 30000 NPHIA = 98340 NUMBND = 74 NUMANG = 174 NPTRA = 278 NATYP = 37 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 40 40 40 | Direct force subcell size = 5.1689 5.1689 5.1689 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 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 = 1, ntpr = 50, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0 ioutfm = 0, 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 = 4000, ncyc = 2000, 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 = 206.756 Box Y = 206.756 Box Z = 206.756 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 216 NFFT2 = 216 NFFT3 = 216 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: 197884 Sum of charges from parm topology file = -0.00000155 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 14121621 | Integers 17731087 | Nonbonded Pairs Initial Allocation: 106249947 | GPU memory information (estimate): | KB of GPU memory in use: 2130046 | KB of CPU memory in use: 786046 -------------------------------------------------------------------------------- 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 = 0.8332E-11 at 2.782960 --------------------------------------------------- |--------------------------------------------------- | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.47 | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION | with 50.0 points per unit in tabled values | Relative Error Limit not exceeded for r .gt. 2.89 |---------------------------------------------------