Dear amber users,
I'm work with a protein which have 25 titrable sites. I've know that it is stable at pH 4, and not stable when pH increase to 8. But when I used the set of parameters on the manual, the ETOT at pH4 went higher than at pH8.
Can you tell me the suitable set of parameters on MD for my protein?
Thank.
---------------------------------
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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 Wed May 16 2007 - 06:07:34 PDT
