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min_all.out
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 12
| Run on 07/06/2013 at 23:45:18
[-O]verwriting output
File Assignments:
| MDIN: min_all.in
| MDOUT: min_all.out
| INPCRD: min_sol.rst
| PARM: protein.prmtop
| RESTRT: min_all.rst
| REFC: protein.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
| MDINFO: mdinfo
Here is the input file:
nimization of the whole system
&cntrl
imin = 1,
maxcyc=1000, ncyc=1000,
ntb=1, ntr=0, cut=9.0
/
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.2
|
| 01/10/2013
|
| 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:
| [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., 2012, (In prep).
|
| - 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 Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla K20m
| CUDA Device Global Mem Size: 4799 MB
| CUDA Device Num Multiprocessors: 13
| CUDA Device Core Freq: 0.71 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| MKL
| CUDA
| Largest sphere to fit in unit cell has radius = 40.660
| New format PARM file being parsed.
| Version = 1.000 Date = 07/06/13 Time = 23:44:58
| 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 = 54782 NTYPES = 19 NBONH = 51054 MBONA = 3827
NTHETH = 8404 MTHETA = 5221 NPHIH = 16472 MPHIA = 12953
NHPARM = 0 NPARM = 0 NNB = 104275 NRES = 16258
NBONA = 3827 NTHETA = 5221 NPHIA = 12953 NUMBND = 63
NUMANG = 131 NPTRA = 45 NATYP = 44 NPHB = 1
IFBOX = 1 NMXRS = 74 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 18 16 17
| Direct force subcell size = 5.1619 5.0825 5.1869
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 = 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 = 9.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 1000, 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 = 92.915 Box Y = 81.320 Box Z = 88.178
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 96 NFFT2 = 84 NFFT3 = 96
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
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: 15786
Sum of charges from parm topology file = -0.00000015
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 1338978
| Integers 1842781
| Nonbonded Pairs Initial Allocation: 12490296
| GPU memory information (estimate):
| KB of GPU memory in use: 115035
| KB of CPU memory in use: 60603
--------------------------------------------------------------------------------
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 = 0.8314E-11 at 2.736960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.39
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.84
|---------------------------------------------------
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.9977E+05 6.1904E-01 5.2574E+01 C1D 7352
BOND = 13369.4817 ANGLE = 1149.1276 DIHED = 4591.6457
VDWAALS = 26933.0080 EEL = -262933.9817 HBOND = 0.0000
1-4 VDW = 1654.3459 1-4 EEL = 15462.9706 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -2.0027E+05 7.2316E-01 1.4195E+01 C 5278
BOND = 13472.0348 ANGLE = 1177.4979 DIHED = 4597.3961
VDWAALS = 27217.6158 EEL = -263750.6183 HBOND = 0.0000
1-4 VDW = 1611.5261 1-4 EEL = 15404.4665 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -2.0070E+05 1.0399E+00 3.2974E+01 C 5278
BOND = 13566.8401 ANGLE = 1189.3729 DIHED = 4593.2654
VDWAALS = 27521.7038 EEL = -264538.5040 HBOND = 0.0000
1-4 VDW = 1591.0937 1-4 EEL = 15375.4231 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
150 -2.0113E+05 3.7691E-01 1.3161E+01 C1D 7352
BOND = 13617.3453 ANGLE = 1196.3137 DIHED = 4587.6567
VDWAALS = 27819.2393 EEL = -265284.8257 HBOND = 0.0000
1-4 VDW = 1578.5814 1-4 EEL = 15356.8868 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -2.0150E+05 8.0537E-01 6.9412E+01 C1D 7352
BOND = 13695.0634 ANGLE = 1206.5622 DIHED = 4581.8560
VDWAALS = 28113.4326 EEL = -266008.3882 HBOND = 0.0000
1-4 VDW = 1569.6870 1-4 EEL = 15344.5458 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
250 -2.0186E+05 2.3555E-01 6.9156E+00 C1D 7352
BOND = 13751.3080 ANGLE = 1198.6621 DIHED = 4576.4984
VDWAALS = 28382.4095 EEL = -266664.6735 HBOND = 0.0000
1-4 VDW = 1563.4020 1-4 EEL = 15336.7868 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -2.0217E+05 7.4326E-01 1.0730E+02 CG 4093
BOND = 13825.9262 ANGLE = 1199.2160 DIHED = 4571.5539
VDWAALS = 28645.9048 EEL = -267303.6931 HBOND = 0.0000
1-4 VDW = 1558.2528 1-4 EEL = 15330.5170 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
350 -2.0248E+05 2.3879E-01 1.0033E+01 C1D 7352
BOND = 13868.4621 ANGLE = 1201.4445 DIHED = 4567.4047
VDWAALS = 28886.7842 EEL = -267886.7109 HBOND = 0.0000
1-4 VDW = 1553.9248 1-4 EEL = 15325.5967 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
400 -2.0277E+05 6.7827E-01 1.0044E+02 CG 4093
BOND = 13929.8513 ANGLE = 1207.0454 DIHED = 4563.4949
VDWAALS = 29128.1371 EEL = -268465.8220 HBOND = 0.0000
1-4 VDW = 1550.1621 1-4 EEL = 15321.1886 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
450 -2.0303E+05 8.7891E-01 8.5289E+01 CG 4093
BOND = 13986.3122 ANGLE = 1211.5333 DIHED = 4560.0462
VDWAALS = 29356.8648 EEL = -269008.3530 HBOND = 0.0000
1-4 VDW = 1547.0520 1-4 EEL = 15318.3992 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
500 -2.0330E+05 5.3792E-01 4.6921E+01 C1D 7352
BOND = 14033.8747 ANGLE = 1200.3854 DIHED = 4556.5705
VDWAALS = 29584.2430 EEL = -269535.4241 HBOND = 0.0000
1-4 VDW = 1544.6107 1-4 EEL = 15316.3462 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
550 -2.0354E+05 8.0199E-01 1.1773E+02 CG 4093
BOND = 14090.0878 ANGLE = 1200.0972 DIHED = 4553.3593
VDWAALS = 29806.9786 EEL = -270043.2212 HBOND = 0.0000
1-4 VDW = 1542.4167 1-4 EEL = 15314.3384 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
600 -2.0378E+05 3.4488E-01 2.6558E+01 C1D 7352
BOND = 14121.2710 ANGLE = 1202.2102 DIHED = 4550.2607
VDWAALS = 30025.6918 EEL = -270533.0545 HBOND = 0.0000
1-4 VDW = 1540.3293 1-4 EEL = 15311.0922 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
650 -2.0400E+05 2.0001E-01 8.1941E+00 C1D 7352
BOND = 14166.0050 ANGLE = 1198.4075 DIHED = 4547.1462
VDWAALS = 30236.3830 EEL = -270998.6228 HBOND = 0.0000
1-4 VDW = 1538.6547 1-4 EEL = 15309.1691 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
700 -2.0421E+05 3.6790E-01 3.1406E+01 C1D 7352
BOND = 14212.2771 ANGLE = 1196.7110 DIHED = 4544.0276
VDWAALS = 30442.9057 EEL = -271450.2324 HBOND = 0.0000
1-4 VDW = 1537.0461 1-4 EEL = 15307.1221 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
750 -2.0441E+05 5.7222E-01 6.9468E+01 CG 4093
BOND = 14258.8765 ANGLE = 1195.8820 DIHED = 4540.8703
VDWAALS = 30645.3105 EEL = -271889.4504 HBOND = 0.0000
1-4 VDW = 1535.4454 1-4 EEL = 15305.3068 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
800 -2.0461E+05 1.8792E-01 7.6162E+00 C1D 7352
BOND = 14289.5780 ANGLE = 1197.0822 DIHED = 4537.7366
VDWAALS = 30838.2936 EEL = -272305.4841 HBOND = 0.0000
1-4 VDW = 1533.7942 1-4 EEL = 15302.8517 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
850 -2.0479E+05 5.1060E-01 4.6001E+01 CG 4093
BOND = 14330.9378 ANGLE = 1200.4068 DIHED = 4534.5555
VDWAALS = 31028.5465 EEL = -272713.7897 HBOND = 0.0000
1-4 VDW = 1532.2355 1-4 EEL = 15300.6377 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
900 -2.0497E+05 2.1642E-01 1.3821E+01 C1D 7352
BOND = 14366.1940 ANGLE = 1194.8624 DIHED = 4531.5382
VDWAALS = 31207.7413 EEL = -273097.1516 HBOND = 0.0000
1-4 VDW = 1530.9535 1-4 EEL = 15299.3019 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
950 -2.0513E+05 4.0251E-01 3.4437E+01 C1D 7352
BOND = 14404.9035 ANGLE = 1193.9081 DIHED = 4528.7486
VDWAALS = 31381.5876 EEL = -273467.3229 HBOND = 0.0000
1-4 VDW = 1529.7506 1-4 EEL = 15297.5200 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -2.0529E+05 5.8288E-01 5.2352E+01 C1D 7352
BOND = 14442.8232 ANGLE = 1193.5758 DIHED = 4526.1911
VDWAALS = 31548.4754 EEL = -273820.7443 HBOND = 0.0000
1-4 VDW = 1528.6846 1-4 EEL = 15295.8412 RESTRAINT = 0.0000
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -2.0529E+05 5.8288E-01 5.2352E+01 C1D 7352
BOND = 14442.8232 ANGLE = 1193.5758 DIHED = 4526.1911
VDWAALS = 31548.4754 EEL = -273820.7443 HBOND = 0.0000
1-4 VDW = 1528.6846 1-4 EEL = 15295.8412 RESTRAINT = 0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 4.62 52.74
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 0.00 0.00
| Other 4.14 47.26
| ------------------------------
| Total 8.75
| 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 0.01
| ---------------------------------
| Total 0.00 0.01
| 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 1 steps:
| Elapsed(s) = 210.89 Per Step(ms) = 210888.15
| ns/day = 0.00 seconds/ns = **********
|
| Average timings for all steps:
| Elapsed(s) = 210.89 Per Step(ms) = 210888.15
| ns/day = 0.00 seconds/ns = **********
| -----------------------------------------------------
| Setup CPU time: 1.75 seconds
| NonSetup CPU time: 8.75 seconds
| Total CPU time: 10.50 seconds 0.00 hours
| Setup wall time: 2 seconds
| NonSetup wall time: 211 seconds
| Total wall time: 213 seconds 0.06 hours
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