------------------------------------------------------- Amber 20 PMEMD 2020 ------------------------------------------------------- | PMEMD implementation of SANDER, Release 18 | Compiled date/time: Mon Apr 27 22:19:54 2020 | Run on 02/27/2022 at 21:51:12 | Executable path: /home/allan/programas/amber20/bin/pmemd.cuda_SPFP | Working directory: /home/allan/work/GH1/MD/crystal_1GNXA_A.pdb/run-md | Hostname: gn030 [-O]verwriting output File Assignments: | MDIN: nvt.mdin | MDOUT: nvt.out | INPCRD: min-1.restrt | PARM: ../setup/x_solv.prmtop | RESTRT: nvt.restrt | REFC: min-1.restrt | MDVEL: mdvel | MDEN: mden | MDCRD: output/nvt.mdcrd | MDINFO: mdinfo | MDFRC: mdfrc Here is the input file: Equilibration nvt run &cntrl ntpr = 1000, ntwx = 10000, ntwr = 5000, ntx = 1, irest = 0, ioutfm = 1, ntxo = 2, jfastw = 0, tol = 0.000001 imin = 0, nstlim = 500000, dt = 0.002, ntb = 1, ntt = 3, ig = -1, gamma_ln = 5.0, tempi = 0.0, temp0 = 300.00, ntc = 2, ntf = 2, cut = 9, ntr = 1, restraint_wt=10 restraintmask=':1-447' / Note: ig = -1. Setting random seed to 873994 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: not set | CUDA Capable Devices Detected: 2 | CUDA Device ID in use: 0 | CUDA Device Name: Tesla K20m | CUDA Device Global Mem Size: 4743 MB | CUDA Device Num Multiprocessors: 13 | CUDA Device Core Freq: 0.71 GHz | |-------------------------------------------------------- | Conditional Compilation Defines Used: | PUBFFT | BINTRAJ | CUDA | EMIL | Largest sphere to fit in unit cell has radius = 34.668 | New format PARM file being parsed. | Version = 1.000 Date = 02/27/22 Time = 21:07:55 | 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 = 41384 NTYPES = 18 NBONH = 37832 MBONA = 3597 NTHETH = 7541 MTHETA = 4919 NPHIH = 15660 MPHIA = 15131 NHPARM = 0 NPARM = 0 NNB = 83684 NRES = 12008 NBONA = 3597 NTHETA = 4919 NPHIA = 15131 NUMBND = 67 NUMANG = 152 NPTRA = 192 NATYP = 37 NPHB = 1 IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Coordinate Index Table dimensions: 15 15 15 | Direct force subcell size = 5.6613 5.6613 5.6613 BOX TYPE: TRUNCATED OCTAHEDRON -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name 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 = 1000, ntrx = 1, ntwr = 5000 iwrap = 0, ntwx = 10000, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 1, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 9.00000, intdiel = 1.00000 Frozen or restrained atoms: ibelly = 0, ntr = 1 restraint_wt = 10.00000 Molecular dynamics: nstlim = 500000, nscm = 0, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = -1.00000 Langevin dynamics temperature regulation: ig = 873994 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 5.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00000 | Intermolecular bonds treatment: | no_intermolecular_bonds = 1 | Energy averages sample interval: | ene_avg_sampling = 1000 Ewald parameters: verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 vdwmeth = 1, eedmeth = 1, netfrc = 1 Box X = 84.920 Box Y = 84.920 Box Z = 84.920 Alpha = 109.471 Beta = 109.471 Gamma = 109.471 NFFT1 = 96 NFFT2 = 96 NFFT3 = 96 Cutoff= 9.000 Tol =0.100E-04 Ewald Coefficient = 0.30768 Interpolation order = 4 LOADING THE CONSTRAINED ATOMS AS GROUPS 5. REFERENCE ATOM COORDINATES default_name Mask :1-447; matches 6823 atoms -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- default_name begin time read from input coords = 0.000 ps Number of triangulated 3-point waters found: 11500 Sum of charges from parm topology file = -0.00000019 Forcing neutrality... | Dynamic Memory, Types Used: | Reals 1338881 | Integers 1798402 | Nonbonded Pairs Initial Allocation: 9435552 | GPU memory information (estimate): | KB of GPU memory in use: 363931 | KB of CPU memory in use: 94555 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -137453.9099 EKtot = 0.0000 EPtot = -137453.9099 BOND = 260.3557 ANGLE = 1077.4926 DIHED = 4885.9214 1-4 NB = 1368.7068 1-4 EEL = 15393.0590 VDWAALS = 68247.4758 EELEC = -228686.9212 EHBOND = 0.0000 RESTRAINT = 0.0000 ------------------------------------------------------------------------------