Dear amber users,
I'm working with a protein with 175 aa ( 25 titrable sites) which is stable at pH 4.
I make MD at pH 4, 6, 8
But the result showed that the ETOT at pH 4 is higher than at pH 8.
I've attached the output file of MD here.
Can you tell me the reason of this ? Thank you very much.
Here is the input file:
Heating up the system equilibration stage 1
&cntrl
icnstph=1, solvph=4, ntcnstph=5,
cut=30, scee=1.2, igb=2, saltcon=0.1,
nstlim=5000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000,
ntwx=5000,
tempi =100.0, temp0=300.0, ntt=1, tautp=2.0, ig=209858,
ntb=0, ntp=0,
ntc=2, ntf=2,
nrespa=1,
&end
Constant temperature equilibration stage 2
&cntrl
nstlim=5000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000,
ntwx=5000,
temp0=300.0, ntt=1, tautp=2.0,
ntb=0,
ntc=2, ntf=2,
nrespa=1,
icnstph=1, solvph=4, ntcnstph=5,
cut=30, scee=1.2, igb=2, saltcon=0.1,
&end
---------------------------------
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-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 05/03/2007 at 17:15:33
[-O]verwriting output
File Assignments:
| MDIN: md1_4.in
| MDOUT: md1_4.out
|INPCRD: min2.rst
| PARM: hgcsf.prmtop
|RESTRT: md1_4.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md1_4.prmcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Heating up the system equilibration stage 1
&cntrl
icnstph=1, solvph=4, ntcnstph=5,
cut=30, scee=1.2, igb=2, saltcon=0.1,
nstlim=5000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000, ntwx=5000,
tempi =100.0, temp0=300.0, ntt=1, tautp=2.0, ig=209858,
ntb=0, ntp=0,
ntc=2, ntf=2,
nrespa=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 04/27/07 Time = 08:46:40
NATOM = 2712 NTYPES = 14 NBONH = 1392 MBONA = 1352
NTHETH = 3138 MTHETA = 1842 NPHIH = 5859 MPHIA = 3314
NHPARM = 0 NPARM = 0 NNB = 15026 NRES = 175
NBONA = 1352 NTHETA = 1842 NPHIA = 3314 NUMBND = 41
NUMANG = 93 NPTRA = 41 NATYP = 27 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 71899
| Hollerith 16449
| Integer 157696
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 1241 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
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 = 500, ntrx = 1, ntwr = 5000
iwrap = 0, ntwx = 5000, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 2, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 30.00000, intdiel = 1.00000
saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000
gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 5000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 100.00000, tautp = 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Constant pH options:
ntcnstph = 5
solvph = 4.00000
reading charge increments from file: cpin
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 121.40 PRESS = 0.0
Etot = -4524.5687 EKtot = 812.7479 EPtot = -5337.3166
BOND = 82.6300 ANGLE = 426.8582 DIHED = 1139.5759
1-4 NB = 529.1812 1-4 EEL = 8036.8677 VDWAALS = -1383.3154
EELEC = -11595.9623 EGB = -2573.1520 RESTRAINT = 0.0000
DV/DL = 0.0000
------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 116.25 PRESS = 0.0
Etot = -3850.4438 EKtot = 778.2783 EPtot = -4628.7221
BOND = 239.7520 ANGLE = 774.9724 DIHED = 1212.1801
1-4 NB = 524.5450 1-4 EEL = 7583.2813 VDWAALS = -1270.8262
EELEC = -11285.0822 EGB = -2407.5446 RESTRAINT = 0.0000
DV/DL = 14.2150
------------------------------------------------------------------------------
KE Trans = 1.6863 KE Rot = 2.4693 C.O.M. Vel = 0.013375
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 155.40 PRESS = 0.0
Etot = -3319.1848 EKtot = 1040.3840 EPtot = -4359.5688
BOND = 286.8442 ANGLE = 897.1772 DIHED = 1237.0204
1-4 NB = 555.7013 1-4 EEL = 7574.8535 VDWAALS = -1209.0318
EELEC = -11727.9902 EGB = -1974.1434 RESTRAINT = 0.0000
DV/DL = 2.2642
------------------------------------------------------------------------------
NSTEP = 1500 TIME(PS) = 3.000 TEMP(K) = 187.28 PRESS = 0.0
Etot = -2889.5521 EKtot = 1253.8314 EPtot = -4143.3835
BOND = 317.1077 ANGLE = 1006.2786 DIHED = 1282.4405
1-4 NB = 561.6622 1-4 EEL = 7550.9732 VDWAALS = -1206.6495
EELEC = -11381.9239 EGB = -2273.2722 RESTRAINT = 0.0000
DV/DL = 23.6613
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 210.49 PRESS = 0.0
Etot = -2537.3869 EKtot = 1409.1968 EPtot = -3946.5837
BOND = 370.8121 ANGLE = 1088.9947 DIHED = 1322.2951
1-4 NB = 567.8730 1-4 EEL = 7517.1037 VDWAALS = -1231.6665
EELEC = -11275.0435 EGB = -2306.9522 RESTRAINT = 0.0000
DV/DL = 27.1502
------------------------------------------------------------------------------
NSTEP = 2500 TIME(PS) = 5.000 TEMP(K) = 227.68 PRESS = 0.0
Etot = -2288.8449 EKtot = 1524.3072 EPtot = -3813.1521
BOND = 423.6113 ANGLE = 1155.4365 DIHED = 1336.5223
1-4 NB = 551.0084 1-4 EEL = 7546.6942 VDWAALS = -1202.8698
EELEC = -11247.1797 EGB = -2376.3753 RESTRAINT = 0.0000
DV/DL = 9.8751
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 244.31 PRESS = 0.0
Etot = -2081.2581 EKtot = 1635.5951 EPtot = -3716.8532
BOND = 417.2066 ANGLE = 1222.5874 DIHED = 1355.8654
1-4 NB = 572.8868 1-4 EEL = 7534.1649 VDWAALS = -1185.3464
EELEC = -11539.0600 EGB = -2095.1579 RESTRAINT = 0.0000
DV/DL = 26.1674
------------------------------------------------------------------------------
NSTEP = 3500 TIME(PS) = 7.000 TEMP(K) = 251.91 PRESS = 0.0
Etot = -1923.9164 EKtot = 1686.5094 EPtot = -3610.4258
BOND = 407.8100 ANGLE = 1290.2356 DIHED = 1368.0743
1-4 NB = 580.1130 1-4 EEL = 7600.3718 VDWAALS = -1172.6824
EELEC = -11485.9476 EGB = -2198.4005 RESTRAINT = 0.0000
DV/DL = 2.5323
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 270.25 PRESS = 0.0
Etot = -1778.5058 EKtot = 1809.2735 EPtot = -3587.7793
BOND = 439.4280 ANGLE = 1315.7330 DIHED = 1341.4831
1-4 NB = 580.5735 1-4 EEL = 7539.8305 VDWAALS = -1172.2805
EELEC = -11256.8931 EGB = -2375.6538 RESTRAINT = 0.0000
DV/DL = 4.7344
------------------------------------------------------------------------------
NSTEP = 4500 TIME(PS) = 9.000 TEMP(K) = 275.18 PRESS = 0.0
Etot = -1678.3874 EKtot = 1842.2650 EPtot = -3520.6524
BOND = 461.7616 ANGLE = 1298.2393 DIHED = 1364.2592
1-4 NB = 589.2946 1-4 EEL = 7584.8395 VDWAALS = -1162.9767
EELEC = -11413.5737 EGB = -2242.4961 RESTRAINT = 0.0000
DV/DL = 2.4125
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 271.50 PRESS = 0.0
Etot = -1596.5179 EKtot = 1817.6498 EPtot = -3414.1677
BOND = 480.0920 ANGLE = 1411.8461 DIHED = 1376.4157
1-4 NB = 583.7661 1-4 EEL = 7595.9330 VDWAALS = -1190.4602
EELEC = -11097.7405 EGB = -2574.0198 RESTRAINT = 0.0000
DV/DL = 4.8245
------------------------------------------------------------------------------
A V E R A G E S O V E R 5000 S T E P S
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 211.06 PRESS = 0.0
Etot = -2540.9100 EKtot = 1412.9996 EPtot = -3953.9096
BOND = 367.4880 ANGLE = 1107.8138 DIHED = 1305.7246
1-4 NB = 562.4813 1-4 EEL = 7586.2920 VDWAALS = -1211.0300
EELEC = -11435.5052 EGB = -2237.1741 RESTRAINT = 0.0000
DV/DL = 1.3584
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 58.36 PRESS = 0.0
Etot = 823.3281 EKtot = 390.7420 EPtot = 433.6677
BOND = 85.7909 ANGLE = 213.7844 DIHED = 56.1649
1-4 NB = 18.2183 1-4 EEL = 68.4757 VDWAALS = 52.7199
EELEC = 204.3768 EGB = 165.4467 RESTRAINT = 0.0000
DV/DL = 4.0330
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Calc gb radii 2033.26 (20.66% of Gen B)
| Calc gb diag 3656.13 (37.15% of Gen B)
| Calc gb off-diag 4150.76 (42.18% of Gen B)
| Gen Born time 9840.23 (100.0% of Nonbo)
| Nonbond force 9840.23 (99.57% of Force)
| Bond/Angle/Dihedral 42.27 ( 0.43% of Force)
| Force time 9882.63 (100.0% of Runmd)
| Shake time 1.95 ( 0.02% of Runmd)
| Verlet update time 2.17 ( 0.02% of Runmd)
| Runmd Time 9886.92 (100.0% of Total)
| Total time 9887.21 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 17:15:33.902 on 05/03/2007
| Setup done at 17:15:34.203 on 05/03/2007
| Run done at 20:00:21.121 on 05/03/2007
| wallclock() was called 100024 times
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 04/27/2007 at 16:25:53
[-O]verwriting output
File Assignments:
| MDIN: md1.in
| MDOUT: md1.out
|INPCRD: min2.rst
| PARM: hgcsf.prmtop
|RESTRT: md1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md1.prmcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Heating up the system equilibration stage 1
&cntrl
icnstph=1, solvph=8, ntcnstph=5,
cut=30, scee=1.2, igb=2, saltcon=0.1,
nstlim=5000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000, ntwx=5000,
tempi =100.0, temp0=300.0, ntt=1, tautp=2.0, ig=209858,
ntb=0, ntp=0,
ntc=2, ntf=2,
nrespa=1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 04/27/07 Time = 08:46:40
NATOM = 2712 NTYPES = 14 NBONH = 1392 MBONA = 1352
NTHETH = 3138 MTHETA = 1842 NPHIH = 5859 MPHIA = 3314
NHPARM = 0 NPARM = 0 NNB = 15026 NRES = 175
NBONA = 1352 NTHETA = 1842 NPHIA = 3314 NUMBND = 41
NUMANG = 93 NPTRA = 41 NATYP = 27 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 71899
| Hollerith 16449
| Integer 157696
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 1241 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
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 = 500, ntrx = 1, ntwr = 5000
iwrap = 0, ntwx = 5000, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 2, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 30.00000, intdiel = 1.00000
saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000
gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 5000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 100.00000, tautp = 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Constant pH options:
ntcnstph = 5
solvph = 8.00000
reading charge increments from file: cpin
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 121.40 PRESS = 0.0
Etot = -4524.5687 EKtot = 812.7479 EPtot = -5337.3166
BOND = 82.6300 ANGLE = 426.8582 DIHED = 1139.5759
1-4 NB = 529.1812 1-4 EEL = 8036.8677 VDWAALS = -1383.3154
EELEC = -11595.9623 EGB = -2573.1520 RESTRAINT = 0.0000
DV/DL = 0.0000
------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 117.13 PRESS = 0.0
Etot = -3967.1514 EKtot = 784.1566 EPtot = -4751.3080
BOND = 239.5311 ANGLE = 772.9195 DIHED = 1210.2937
1-4 NB = 521.1331 1-4 EEL = 7871.6497 VDWAALS = -1273.2408
EELEC = -11712.0822 EGB = -2381.5119 RESTRAINT = 0.0000
DV/DL = 9.4624
------------------------------------------------------------------------------
KE Trans = 1.6962 KE Rot = 2.4853 C.O.M. Vel = 0.013414
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 154.57 PRESS = 0.0
Etot = -3431.2318 EKtot = 1034.8325 EPtot = -4466.0644
BOND = 282.3614 ANGLE = 900.3191 DIHED = 1254.0546
1-4 NB = 544.2663 1-4 EEL = 7838.4691 VDWAALS = -1228.3495
EELEC = -11811.9393 EGB = -2245.2461 RESTRAINT = 0.0000
DV/DL = 5.2077
------------------------------------------------------------------------------
NSTEP = 1500 TIME(PS) = 3.000 TEMP(K) = 183.23 PRESS = 0.0
Etot = -3011.9814 EKtot = 1226.6769 EPtot = -4238.6582
BOND = 307.3392 ANGLE = 1026.4449 DIHED = 1275.0764
1-4 NB = 560.1927 1-4 EEL = 7865.4800 VDWAALS = -1227.1356
EELEC = -11669.5708 EGB = -2376.4850 RESTRAINT = 0.0000
DV/DL = 33.5049
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 207.94 PRESS = 0.0
Etot = -2659.1507 EKtot = 1392.1258 EPtot = -4051.2765
BOND = 317.6803 ANGLE = 1127.0615 DIHED = 1315.6136
1-4 NB = 574.6931 1-4 EEL = 7865.3743 VDWAALS = -1198.4091
EELEC = -11803.4290 EGB = -2249.8611 RESTRAINT = 0.0000
DV/DL = 16.0559
------------------------------------------------------------------------------
NSTEP = 2500 TIME(PS) = 5.000 TEMP(K) = 233.46 PRESS = 0.0
Etot = -2394.4786 EKtot = 1562.9680 EPtot = -3957.4467
BOND = 360.4889 ANGLE = 1169.4712 DIHED = 1330.5428
1-4 NB = 574.9756 1-4 EEL = 7844.7816 VDWAALS = -1198.7460
EELEC = -11697.9903 EGB = -2340.9704 RESTRAINT = 0.0000
DV/DL = 9.3819
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 245.63 PRESS = 0.0
Etot = -2189.7512 EKtot = 1644.4701 EPtot = -3834.2213
BOND = 398.2996 ANGLE = 1202.0022 DIHED = 1353.4123
1-4 NB = 584.6640 1-4 EEL = 7868.4710 VDWAALS = -1168.7394
EELEC = -11871.9489 EGB = -2200.3821 RESTRAINT = 0.0000
DV/DL = 1.5969
------------------------------------------------------------------------------
NSTEP = 3500 TIME(PS) = 7.000 TEMP(K) = 253.00 PRESS = 0.0
Etot = -2030.4200 EKtot = 1693.8146 EPtot = -3724.2346
BOND = 466.6690 ANGLE = 1279.3858 DIHED = 1365.1374
1-4 NB = 561.6640 1-4 EEL = 7838.5333 VDWAALS = -1185.0318
EELEC = -11909.6087 EGB = -2140.9835 RESTRAINT = 0.0000
DV/DL = 2.5612
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 265.79 PRESS = 0.0
Etot = -1902.2581 EKtot = 1779.4306 EPtot = -3681.6887
BOND = 440.7051 ANGLE = 1329.1910 DIHED = 1367.4069
1-4 NB = 576.6099 1-4 EEL = 7861.8697 VDWAALS = -1162.1380
EELEC = -11847.7606 EGB = -2247.5728 RESTRAINT = 0.0000
DV/DL = 8.6596
------------------------------------------------------------------------------
NSTEP = 4500 TIME(PS) = 9.000 TEMP(K) = 278.07 PRESS = 0.0
Etot = -1800.9881 EKtot = 1861.6335 EPtot = -3662.6216
BOND = 461.1859 ANGLE = 1300.3271 DIHED = 1389.5337
1-4 NB = 566.9224 1-4 EEL = 7930.9635 VDWAALS = -1162.7527
EELEC = -11572.7542 EGB = -2576.0475 RESTRAINT = 0.0000
DV/DL = -2.2457
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 281.36 PRESS = 0.0
Etot = -1738.3250 EKtot = 1883.6705 EPtot = -3621.9955
BOND = 478.9239 ANGLE = 1335.7859 DIHED = 1372.1196
1-4 NB = 576.5636 1-4 EEL = 7963.5273 VDWAALS = -1163.3506
EELEC = -11648.6024 EGB = -2536.9627 RESTRAINT = 0.0000
DV/DL = 10.7254
------------------------------------------------------------------------------
A V E R A G E S O V E R 5000 S T E P S
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 211.24 PRESS = 0.0
Etot = -2652.1963 EKtot = 1414.2275 EPtot = -4066.4237
BOND = 365.8176 ANGLE = 1104.8120 DIHED = 1312.2024
1-4 NB = 563.2613 1-4 EEL = 7874.1868 VDWAALS = -1207.2051
EELEC = -11822.3583 EGB = -2257.1405 RESTRAINT = 0.0000
DV/DL = 1.6586
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 58.76 PRESS = 0.0
Etot = 808.9008 EKtot = 393.3986 EPtot = 416.7100
BOND = 86.4467 ANGLE = 211.8968 DIHED = 60.0205
1-4 NB = 18.8324 1-4 EEL = 44.2133 VDWAALS = 53.7504
EELEC = 164.1576 EGB = 162.6049 RESTRAINT = 0.0000
DV/DL = 4.6651
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Calc gb radii 2184.94 (21.83% of Gen B)
| Calc gb diag 3665.27 (36.62% of Gen B)
| Calc gb off-diag 4158.28 (41.55% of Gen B)
| Gen Born time 10008.57 (100.0% of Nonbo)
| Nonbond force 10008.57 (99.58% of Force)
| Bond/Angle/Dihedral 42.20 ( 0.42% of Force)
| Force time 10050.91 (99.78% of Runmd)
| Shake time 1.96 ( 0.02% of Runmd)
| Verlet update time 4.65 ( 0.05% of Runmd)
| Other 15.77 ( 0.16% of Runmd)
| Runmd Time 10073.27 (100.0% of Total)
| Total time 10073.57 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 16:25:53.156 on 04/27/2007
| Setup done at 16:25:53.453 on 04/27/2007
| Run done at 19:13:46.730 on 04/27/2007
| wallclock() was called 100024 times
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 05/03/2007 at 20:00:21
[-O]verwriting output
File Assignments:
| MDIN: md2_4.in
| MDOUT: md2_4.out
|INPCRD: md1_4.rst
| PARM: hgcsf.prmtop
|RESTRT: md2_4.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md2_4.prmcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Constant pressure constant temperature equilibration stage 2
&cntrl
nstlim=5000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
temp0=300.0, ntt=1, tautp=2.0,
ntb=0,
ntc=2, ntf=2,
nrespa=1,
icnstph=1, solvph=4, ntcnstph=5,
cut=30, scee=1.2, igb=2, saltcon=0.1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 04/27/07 Time = 08:46:40
NATOM = 2712 NTYPES = 14 NBONH = 1392 MBONA = 1352
NTHETH = 3138 MTHETA = 1842 NPHIH = 5859 MPHIA = 3314
NHPARM = 0 NPARM = 0 NNB = 15026 NRES = 175
NBONA = 1352 NTHETA = 1842 NPHIA = 3314 NUMBND = 41
NUMANG = 93 NPTRA = 41 NATYP = 27 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 71899
| Hollerith 16449
| Integer 157696
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 1241 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
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 = 500, ntrx = 1, ntwr = 5000
iwrap = 0, ntwx = 5000, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 2, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 30.00000, intdiel = 1.00000
saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000
gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 5000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Constant pH options:
ntcnstph = 5
solvph = 4.00000
reading charge increments from file: cprestrt1_4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 10.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 11.000 TEMP(K) = 285.02 PRESS = 0.0
Etot = -1533.3126 EKtot = 1908.1974 EPtot = -3441.5100
BOND = 450.3031 ANGLE = 1397.0796 DIHED = 1358.9665
1-4 NB = 586.2499 1-4 EEL = 7552.1162 VDWAALS = -1187.6094
EELEC = -11351.7710 EGB = -2246.8449 RESTRAINT = 0.0000
DV/DL = 19.4606
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 1000 TIME(PS) = 12.000 TEMP(K) = 286.80 PRESS = 0.0
Etot = -1507.1004 EKtot = 1920.0541 EPtot = -3427.1546
BOND = 456.9659 ANGLE = 1412.0115 DIHED = 1345.2220
1-4 NB = 586.6162 1-4 EEL = 7672.4261 VDWAALS = -1179.2965
EELEC = -11300.9773 EGB = -2420.1224 RESTRAINT = 0.0000
DV/DL = 12.1167
------------------------------------------------------------------------------
NSTEP = 1500 TIME(PS) = 13.000 TEMP(K) = 288.04 PRESS = 0.0
Etot = -1496.4441 EKtot = 1928.4015 EPtot = -3424.8456
BOND = 493.9785 ANGLE = 1425.0846 DIHED = 1359.4748
1-4 NB = 559.0965 1-4 EEL = 7771.3228 VDWAALS = -1167.5426
EELEC = -11756.2966 EGB = -2109.9636 RESTRAINT = 0.0000
DV/DL = 2.3519
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 2000 TIME(PS) = 14.000 TEMP(K) = 292.37 PRESS = 0.0
Etot = -1434.2199 EKtot = 1957.3875 EPtot = -3391.6074
BOND = 511.1000 ANGLE = 1416.7754 DIHED = 1358.2178
1-4 NB = 566.7246 1-4 EEL = 7683.5557 VDWAALS = -1134.1889
EELEC = -11082.5323 EGB = -2711.2598 RESTRAINT = 0.0000
DV/DL = 3.4133
------------------------------------------------------------------------------
NSTEP = 2500 TIME(PS) = 15.000 TEMP(K) = 286.17 PRESS = 0.0
Etot = -1407.5821 EKtot = 1915.8606 EPtot = -3323.4427
BOND = 495.7177 ANGLE = 1464.1694 DIHED = 1372.5000
1-4 NB = 587.5913 1-4 EEL = 7657.9657 VDWAALS = -1154.4051
EELEC = -11485.5653 EGB = -2261.4164 RESTRAINT = 0.0000
DV/DL = 1.7577
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 3000 TIME(PS) = 16.000 TEMP(K) = 292.32 PRESS = 0.0
Etot = -1388.6534 EKtot = 1957.0073 EPtot = -3345.6607
BOND = 509.2322 ANGLE = 1477.9798 DIHED = 1339.3522
1-4 NB = 591.9655 1-4 EEL = 7638.8940 VDWAALS = -1139.6063
EELEC = -11690.3819 EGB = -2073.0962 RESTRAINT = 0.0000
DV/DL = 7.9841
------------------------------------------------------------------------------
NSTEP = 3500 TIME(PS) = 17.000 TEMP(K) = 296.87 PRESS = 0.0
Etot = -1382.4918 EKtot = 1987.5117 EPtot = -3370.0036
BOND = 540.8940 ANGLE = 1453.1406 DIHED = 1337.1705
1-4 NB = 579.1882 1-4 EEL = 7684.8667 VDWAALS = -1197.4193
EELEC = -11403.1854 EGB = -2364.6588 RESTRAINT = 0.0000
DV/DL = 8.9171
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 4000 TIME(PS) = 18.000 TEMP(K) = 292.49 PRESS = 0.0
Etot = -1383.4032 EKtot = 1958.1952 EPtot = -3341.5984
BOND = 486.8193 ANGLE = 1494.9606 DIHED = 1405.4801
1-4 NB = 595.0325 1-4 EEL = 7705.3338 VDWAALS = -1201.8786
EELEC = -11709.2333 EGB = -2118.1128 RESTRAINT = 0.0000
DV/DL = 2.7415
------------------------------------------------------------------------------
NSTEP = 4500 TIME(PS) = 19.000 TEMP(K) = 300.94 PRESS = 0.0
Etot = -1378.3451 EKtot = 2014.7513 EPtot = -3393.0964
BOND = 510.1990 ANGLE = 1449.0232 DIHED = 1387.8945
1-4 NB = 589.1110 1-4 EEL = 7726.7900 VDWAALS = -1209.0058
EELEC = -11572.1923 EGB = -2274.9160 RESTRAINT = 0.0000
DV/DL = 3.4703
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 297.39 PRESS = 0.0
Etot = -1340.6977 EKtot = 1990.9933 EPtot = -3331.6910
BOND = 514.3407 ANGLE = 1458.2715 DIHED = 1370.5731
1-4 NB = 577.6254 1-4 EEL = 7635.5460 VDWAALS = -1181.0639
EELEC = -11423.9990 EGB = -2282.9848 RESTRAINT = 0.0000
DV/DL = -0.5278
------------------------------------------------------------------------------
A V E R A G E S O V E R 5000 S T E P S
NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 292.31 PRESS = 0.0
Etot = -1444.5534 EKtot = 1956.9882 EPtot = -3401.5416
BOND = 501.3962 ANGLE = 1431.7872 DIHED = 1368.9120
1-4 NB = 577.8093 1-4 EEL = 7674.0549 VDWAALS = -1171.2597
EELEC = -11425.1870 EGB = -2359.0544 RESTRAINT = 0.0000
DV/DL = 1.3196
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 6.83 PRESS = 0.0
Etot = 74.3284 EKtot = 45.7381 EPtot = 46.5619
BOND = 23.3756 ANGLE = 34.5267 DIHED = 20.3165
1-4 NB = 10.0287 1-4 EEL = 76.1585 VDWAALS = 26.8786
EELEC = 181.9664 EGB = 156.7319 RESTRAINT = 0.0000
DV/DL = 3.8344
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Calc gb radii 2030.11 (20.72% of Gen B)
| Calc gb diag 3650.32 (37.26% of Gen B)
| Calc gb off-diag 4116.36 (42.02% of Gen B)
| Gen Born time 9796.88 (100.0% of Nonbo)
| Nonbond force 9796.88 (99.57% of Force)
| Bond/Angle/Dihedral 42.18 ( 0.43% of Force)
| Force time 9839.21 (100.0% of Runmd)
| Shake time 2.03 ( 0.02% of Runmd)
| Verlet update time 2.21 ( 0.02% of Runmd)
| Runmd Time 9843.54 (100.0% of Total)
| Total time 9843.62 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 20:00:21.130 on 05/03/2007
| Setup done at 20:00:21.217 on 05/03/2007
| Run done at 22:44:24.752 on 05/03/2007
| wallclock() was called 100010 times
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 05/02/2007 at 10:34:05
[-O]verwriting output
File Assignments:
| MDIN: md2.in
| MDOUT: md2.out
|INPCRD: md1.rst
| PARM: hgcsf.prmtop
|RESTRT: md2.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md2.prmcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Constant pressure constant temperature equilibration stage 2
&cntrl
nstlim=5000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
temp0=300.0, ntt=1, tautp=2.0,
ntb=0,
ntc=2, ntf=2,
nrespa=1,
icnstph=1, solvph=8, ntcnstph=5,
cut=30, scee=1.2, igb=2, saltcon=0.1,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 04/27/07 Time = 08:46:40
NATOM = 2712 NTYPES = 14 NBONH = 1392 MBONA = 1352
NTHETH = 3138 MTHETA = 1842 NPHIH = 5859 MPHIA = 3314
NHPARM = 0 NPARM = 0 NNB = 15026 NRES = 175
NBONA = 1352 NTHETA = 1842 NPHIA = 3314 NUMBND = 41
NUMANG = 93 NPTRA = 41 NATYP = 27 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 71899
| Hollerith 16449
| Integer 157696
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 1241 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
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 = 500, ntrx = 1, ntwr = 5000
iwrap = 0, ntwx = 5000, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 2, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 30.00000, intdiel = 1.00000
saltcon = 0.10000, offset = 0.09000, gbalpha= 0.80000
gbbeta = 0.00000, gbgamma = 2.90912, surften = 0.00500
rdt = 0.00000, rgbmax = 25.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 5000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 300.00000, tempi = 0.00000, tautp = 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Constant pH options:
ntcnstph = 5
solvph = 8.00000
reading charge increments from file: cprestrt1
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 10.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 11.000 TEMP(K) = 282.06 PRESS = 0.0
Etot = -1679.6596 EKtot = 1888.3711 EPtot = -3568.0307
BOND = 465.0508 ANGLE = 1421.5299 DIHED = 1375.2944
1-4 NB = 587.4312 1-4 EEL = 7903.4782 VDWAALS = -1152.5214
EELEC = -12082.4192 EGB = -2085.8745 RESTRAINT = 0.0000
DV/DL = 11.5840
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 1000 TIME(PS) = 12.000 TEMP(K) = 289.91 PRESS = 0.0
Etot = -1632.3432 EKtot = 1940.8767 EPtot = -3573.2199
BOND = 470.4091 ANGLE = 1410.1208 DIHED = 1359.1487
1-4 NB = 594.8088 1-4 EEL = 7950.9014 VDWAALS = -1169.7611
EELEC = -11850.9330 EGB = -2337.9145 RESTRAINT = 0.0000
DV/DL = 5.0446
------------------------------------------------------------------------------
NSTEP = 1500 TIME(PS) = 13.000 TEMP(K) = 291.24 PRESS = 0.0
Etot = -1589.5834 EKtot = 1949.8012 EPtot = -3539.3846
BOND = 483.7273 ANGLE = 1436.2567 DIHED = 1367.4220
1-4 NB = 577.2706 1-4 EEL = 7950.5222 VDWAALS = -1189.2312
EELEC = -11998.9813 EGB = -2166.3709 RESTRAINT = 0.0000
DV/DL = 10.4380
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 2000 TIME(PS) = 14.000 TEMP(K) = 284.57 PRESS = 0.0
Etot = -1561.4321 EKtot = 1905.1325 EPtot = -3466.5646
BOND = 543.0623 ANGLE = 1429.6014 DIHED = 1379.5036
1-4 NB = 572.4602 1-4 EEL = 7903.0388 VDWAALS = -1156.1827
EELEC = -11844.6056 EGB = -2293.4426 RESTRAINT = 0.0000
DV/DL = 15.8857
------------------------------------------------------------------------------
NSTEP = 2500 TIME(PS) = 15.000 TEMP(K) = 291.55 PRESS = 0.0
Etot = -1528.5231 EKtot = 1951.9033 EPtot = -3480.4264
BOND = 550.6383 ANGLE = 1435.5116 DIHED = 1349.4036
1-4 NB = 586.7174 1-4 EEL = 7922.0661 VDWAALS = -1175.5502
EELEC = -11725.0398 EGB = -2424.1735 RESTRAINT = 0.0000
DV/DL = 7.9371
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 3000 TIME(PS) = 16.000 TEMP(K) = 287.62 PRESS = 0.0
Etot = -1519.6642 EKtot = 1925.5979 EPtot = -3445.2621
BOND = 547.1556 ANGLE = 1431.7029 DIHED = 1380.7362
1-4 NB = 575.7605 1-4 EEL = 7949.4334 VDWAALS = -1149.7443
EELEC = -11818.2918 EGB = -2362.0146 RESTRAINT = 0.0000
DV/DL = 14.7768
------------------------------------------------------------------------------
NSTEP = 3500 TIME(PS) = 17.000 TEMP(K) = 301.95 PRESS = 0.0
Etot = -1510.7045 EKtot = 2021.4979 EPtot = -3532.2025
BOND = 530.7116 ANGLE = 1409.3994 DIHED = 1392.4435
1-4 NB = 576.8424 1-4 EEL = 7921.8958 VDWAALS = -1220.4618
EELEC = -11782.9286 EGB = -2360.1048 RESTRAINT = 0.0000
DV/DL = 20.4688
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 4000 TIME(PS) = 18.000 TEMP(K) = 301.82 PRESS = 0.0
Etot = -1510.1729 EKtot = 2020.6299 EPtot = -3530.8029
BOND = 512.7248 ANGLE = 1400.5998 DIHED = 1402.7646
1-4 NB = 581.2021 1-4 EEL = 8002.6893 VDWAALS = -1223.4386
EELEC = -11919.6450 EGB = -2287.6998 RESTRAINT = 0.0000
DV/DL = 6.5673
------------------------------------------------------------------------------
NSTEP = 4500 TIME(PS) = 19.000 TEMP(K) = 301.73 PRESS = 0.0
Etot = -1495.6247 EKtot = 2020.0655 EPtot = -3515.6902
BOND = 555.9723 ANGLE = 1425.9297 DIHED = 1358.8031
1-4 NB = 575.8175 1-4 EEL = 7865.6001 VDWAALS = -1245.0702
EELEC = -11896.2612 EGB = -2156.4814 RESTRAINT = 0.0000
DV/DL = 13.6305
------------------------------------------------------------------------------
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
Translational and rotational motion removed
KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 300.00 PRESS = 0.0
Etot = -1507.4736 EKtot = 2008.4524 EPtot = -3515.9260
BOND = 518.8800 ANGLE = 1487.4432 DIHED = 1373.2097
1-4 NB = 590.9159 1-4 EEL = 7951.5640 VDWAALS = -1254.5249
EELEC = -11947.4797 EGB = -2235.9341 RESTRAINT = 0.0000
DV/DL = 6.8981
------------------------------------------------------------------------------
A V E R A G E S O V E R 5000 S T E P S
NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 292.83 PRESS = 0.0
Etot = -1564.5359 EKtot = 1960.4253 EPtot = -3524.9612
BOND = 502.1014 ANGLE = 1423.3621 DIHED = 1379.7278
1-4 NB = 581.5625 1-4 EEL = 7943.7138 VDWAALS = -1183.3684
EELEC = -11944.3882 EGB = -2227.6723 RESTRAINT = 0.0000
DV/DL = 1.7686
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 7.18 PRESS = 0.0
Etot = 66.7850 EKtot = 48.0470 EPtot = 36.6836
BOND = 21.2971 ANGLE = 35.9549 DIHED = 15.8015
1-4 NB = 10.4570 1-4 EEL = 36.0938 VDWAALS = 34.0597
EELEC = 179.2281 EGB = 173.5190 RESTRAINT = 0.0000
DV/DL = 4.6169
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Calc gb radii 2045.39 (20.68% of Gen B)
| Calc gb diag 3680.51 (37.21% of Gen B)
| Calc gb off-diag 4166.20 (42.12% of Gen B)
| Gen Born time 9892.19 (100.0% of Nonbo)
| Nonbond force 9892.19 (99.57% of Force)
| Bond/Angle/Dihedral 42.22 ( 0.42% of Force)
| Force time 9934.55 (100.0% of Runmd)
| Shake time 1.98 ( 0.02% of Runmd)
| Verlet update time 2.30 ( 0.02% of Runmd)
| Runmd Time 9939.07 (100.0% of Total)
| Total time 9939.47 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 10:34:05.156 on 05/02/2007
| Setup done at 10:34:05.557 on 05/02/2007
| Run done at 13:19:44.628 on 05/02/2007
| wallclock() was called 100010 times
-----------------------------------------------------------------------
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Received on Sun May 20 2007 - 06:07:10 PDT
