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|
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 07/12/2011 at 09:04:54
[-O]verwriting output
File Assignments:
| MDIN: run1.in
| MDOUT: run1.out
| INPCRD: run0.rst7
| PARM: ../Struct-mbondi/trpzip2.ff10.mbondi.parm7
| RESTRT: run1.rst7
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: run1.nc
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
short md with igb1
&cntrl
imin = 0, nstlim = 10000, dt = 0.001, nrespa = 1,
ntx=5, irest = 1, ig = -1,
ntwx = 1000, ioutfm = 1, ntpr = 1000, ntwr = 10000,
ntt = 3, gamma_ln = 5, temp0 = 300.0, tempi = 300.0,
ntc = 2, ntf = 2, ntb = 0, cut = 999.0,
igb = 1, saltcon = 0.0, gbsa = 0,
&end
Note: ig = -1. Setting random seed based on wallclock time in microseconds
and disabling the synchronization of random numbers between 1 tasks
to improve performance.
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| New format PARM file being parsed.
| Version = 1.000 Date = 07/12/11 Time = 08:34:45
| 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:
--------------------------------------------------------------------------------
NATOM = 220 NTYPES = 12 NBONH = 104 MBONA = 123
NTHETH = 233 MTHETA = 169 NPHIH = 481 MPHIA = 372
NHPARM = 0 NPARM = 0 NNB = 1211 NRES = 13
NBONA = 123 NTHETA = 169 NPHIA = 372 NUMBND = 31
NUMANG = 68 NPTRA = 35 NATYP = 21 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 10000
iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 1, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.00000, gbgamma = 0.00000, 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 = 10000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 171315
temp0 = 300.00000, tempi = 300.00000, gamma_ln= 5.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1000
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 1.000 ps
Number of triangulated 3-point waters found: 0
| Dynamic Memory, Types Used:
| Reals 9899
| Integers 119322
| Running AMBER/MPI version on 4 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| RE_POSITION Moving by 0.787915 -0.361547 0.358004
NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 310.58 PRESS = 0.0
Etot = -88.9869 EKtot = 171.5762 EPtot = -260.5631
BOND = 30.2604 ANGLE = 100.2719 DIHED = 131.8541
1-4 NB = 40.9369 1-4 EEL = 650.6909 VDWAALS = -79.8350
EELEC = -850.9613 EGB = -283.7809 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by -0.366353 -0.385677 -0.307940
NSTEP = 2000 TIME(PS) = 3.000 TEMP(K) = 313.86 PRESS = 0.0
Etot = -80.9793 EKtot = 173.3891 EPtot = -254.3684
BOND = 35.6636 ANGLE = 102.6118 DIHED = 123.6321
1-4 NB = 41.2398 1-4 EEL = 639.0688 VDWAALS = -71.9564
EELEC = -850.0041 EGB = -274.6240 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by -0.168836 0.086412 0.015309
NSTEP = 3000 TIME(PS) = 4.000 TEMP(K) = 352.68 PRESS = 0.0
Etot = -67.2752 EKtot = 194.8317 EPtot = -262.1069
BOND = 38.5396 ANGLE = 92.6127 DIHED = 128.3893
1-4 NB = 42.8395 1-4 EEL = 657.7879 VDWAALS = -79.5533
EELEC = -842.1625 EGB = -300.5600 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by 0.328082 -0.008404 0.315578
NSTEP = 4000 TIME(PS) = 5.000 TEMP(K) = 288.89 PRESS = 0.0
Etot = -89.5776 EKtot = 159.5932 EPtot = -249.1708
BOND = 49.5508 ANGLE = 108.3589 DIHED = 122.9815
1-4 NB = 41.6255 1-4 EEL = 646.2620 VDWAALS = -71.8875
EELEC = -822.7445 EGB = -323.3175 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by -0.461007 0.206196 -0.373860
NSTEP = 5000 TIME(PS) = 6.000 TEMP(K) = 340.06 PRESS = 0.0
Etot = -67.2116 EKtot = 187.8608 EPtot = -255.0724
BOND = 38.9846 ANGLE = 107.6597 DIHED = 125.3545
1-4 NB = 41.7236 1-4 EEL = 662.6387 VDWAALS = -81.2345
EELEC = -875.5932 EGB = -274.6058 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by 0.581277 0.046247 -0.094222
NSTEP = 6000 TIME(PS) = 7.000 TEMP(K) = 280.12 PRESS = 0.0
Etot = -108.9382 EKtot = 154.7481 EPtot = -263.6863
BOND = 43.8380 ANGLE = 98.0032 DIHED = 127.7448
1-4 NB = 40.4414 1-4 EEL = 645.3672 VDWAALS = -82.8558
EELEC = -858.5229 EGB = -277.7022 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by 0.398818 0.271976 0.444930
NSTEP = 7000 TIME(PS) = 8.000 TEMP(K) = 295.03 PRESS = 0.0
Etot = -102.2957 EKtot = 162.9874 EPtot = -265.2831
BOND = 40.1545 ANGLE = 94.8829 DIHED = 126.4775
1-4 NB = 43.4330 1-4 EEL = 648.1630 VDWAALS = -83.7493
EELEC = -858.2565 EGB = -276.3882 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by 0.148506 -0.380497 -0.670910
NSTEP = 8000 TIME(PS) = 9.000 TEMP(K) = 290.42 PRESS = 0.0
Etot = -99.3741 EKtot = 160.4389 EPtot = -259.8130
BOND = 49.3581 ANGLE = 109.2968 DIHED = 121.6121
1-4 NB = 39.3632 1-4 EEL = 642.0757 VDWAALS = -82.3322
EELEC = -875.6211 EGB = -263.5656 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by -0.532099 -0.042162 0.110563
NSTEP = 9000 TIME(PS) = 10.000 TEMP(K) = 304.77 PRESS = 0.0
Etot = -83.7917 EKtot = 168.3691 EPtot = -252.1608
BOND = 55.9404 ANGLE = 97.5173 DIHED = 121.6542
1-4 NB = 42.6176 1-4 EEL = 660.2676 VDWAALS = -78.5090
EELEC = -882.6452 EGB = -269.0036 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| RE_POSITION Moving by 0.212366 -0.104347 0.028628
NSTEP = 10000 TIME(PS) = 11.000 TEMP(K) = 308.54 PRESS = 0.0
Etot = -90.6731 EKtot = 170.4491 EPtot = -261.1222
BOND = 40.8216 ANGLE = 93.9606 DIHED = 127.7011
1-4 NB = 41.8634 1-4 EEL = 653.1833 VDWAALS = -78.0797
EELEC = -871.8329 EGB = -268.7397 RESTRAINT = 0.0000
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
NSTEP = 10000 TIME(PS) = 11.000 TEMP(K) = 308.49 PRESS = 0.0
Etot = -87.9103 EKtot = 170.4244 EPtot = -258.3347
BOND = 42.3111 ANGLE = 100.5176 DIHED = 125.7401
1-4 NB = 41.6084 1-4 EEL = 650.5505 VDWAALS = -78.9993
EELEC = -858.8344 EGB = -281.2287 RESTRAINT = 0.0000
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 10000 TIME(PS) = 11.000 TEMP(K) = 21.66 PRESS = 0.0
Etot = 13.0818 EKtot = 11.9673 EPtot = 5.0452
BOND = 7.1535 ANGLE = 5.8870 DIHED = 3.1424
1-4 NB = 1.1372 1-4 EEL = 7.4464 VDWAALS = 3.9473
EELEC = 17.3764 EGB = 17.0072 RESTRAINT = 0.0000
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines, Average for All Tasks:
|
| Routine Sec %
| ------------------------------
| DataDistrib 0.07 0.46
| Nonbond 14.37 91.93
| Bond 0.01 0.07
| Angle 0.16 1.03
| Dihedral 0.63 4.05
| Shake 0.02 0.15
| RunMD 0.36 2.29
| Other 0.00 0.01
| ------------------------------
| Total 15.63
| Generalized Born CPU Time, Average for All Tasks:
|
| Routine Sec %
| ------------------------------------
| Radii Calc 3.01 19.27
| Diagonal Calc 5.23 33.45
| Off Diagonal Calc 5.86 37.51
| GBSA LCPO Calc 0.00 0.01
| Radii Distrib 0.20 1.30
| ---------------------------------
| Total 14.31 91.52
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 9000 steps:
| Elapsed(s) = 14.07 Per Step(ms) = 1.56
| ns/day = 55.26 seconds/ns = 1563.40
|
| Average timings for all steps:
| Elapsed(s) = 15.64 Per Step(ms) = 1.56
| ns/day = 55.25 seconds/ns = 1563.67
| -----------------------------------------------------
| Master Setup CPU time: 0.02 seconds
| Master NonSetup CPU time: 15.63 seconds
| Master Total CPU time: 15.65 seconds 0.00 hours
| Master Setup wall time: 0 seconds
| Master NonSetup wall time: 16 seconds
| Master Total wall time: 16 seconds 0.00 hours
|
