Dear all
I see an unusual thing in the simulation output file. the simulation time
doesn't increase monotonically and in some points time was decrease . I
restart the simulation for the second times. Is there a problem with the
simulation?
Best regard
Nasiri
===============================================================
cat mdin.in
equilibration for box
&cntrl
imin=0, ntpr=5000, ntwx=5000,
ntx=5, irest=1,
tempi=298., temp0=298., ntt=3, cut=12,
gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1, nstlim=5000000,
dt=.001, ig=-1,
&end
===============================================================
tail -f md2.out
NSTEP = 3685000 TIME(PS) = 7154.000 TEMP(K) = 296.60 PRESS =
-328.0
Etot = 75.3663 EKtot = 1996.2872 EPtot =
-1920.9210
BOND = 685.6971 ANGLE = 874.3359 DIHED =
173.2846
1-4 NB = 29.6882 1-4 EEL = 942.3203 VDWAALS =
-889.6112
EELEC = -3736.6358 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 276.3988 VIRIAL = 445.3237 VOLUME =
23850.7575
Density =
0.9625
Ewald error estimate: 0.2486E-05
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 2620000 TIME(PS) = 6089.000 TEMP(K) = 298.70 PRESS =
87.8
Etot = 26.8390 EKtot = 2010.4689 EPtot =
-1983.6300
BOND = 657.7941 ANGLE = 864.5939 DIHED =
164.2531
1-4 NB = 34.7123 1-4 EEL = 943.6344 VDWAALS =
-831.5673
EELEC = -3817.0505 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 274.2455 VIRIAL = 229.0013 VOLUME =
23863.1407
Density =
0.9620
Ewald error estimate: 0.1458E-03
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 3675000 TIME(PS) = 7144.000 TEMP(K) = 292.35 PRESS =
-434.8
Etot = -42.2018 EKtot = 1967.6978 EPtot =
-2009.8996
BOND = 695.9076 ANGLE = 866.8796 DIHED =
165.4624
1-4 NB = 32.1543 1-4 EEL = 940.7004 VDWAALS =
-861.2716
EELEC = -3849.7324 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 267.4029 VIRIAL = 490.1511 VOLUME =
23727.4222
Density =
0.9675
Ewald error estimate: 0.7749E-05
------------------------------------------------------------------------------
NSTEP = 3680000 TIME(PS) = 7149.000 TEMP(K) = 293.57 PRESS =
176.7
Etot = 16.0054 EKtot = 1975.8858 EPtot =
-1959.8804
BOND = 705.1786 ANGLE = 863.6585 DIHED =
161.7564
1-4 NB = 30.9969 1-4 EEL = 940.1353 VDWAALS =
-858.4156
EELEC = -3803.1905 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 281.6518 VIRIAL = 191.2233 VOLUME =
23700.5065
Density =
0.9686
Ewald error estimate: 0.5543E-04
------------------------------------------------------------------------------
NSTEP = 3690000 TIME(PS) = 7159.000 TEMP(K) = 294.49 PRESS =
103.7
Etot = 10.5945 EKtot = 1982.0828 EPtot =
-1971.4883
BOND = 695.6595 ANGLE = 866.4718 DIHED =
155.1481
1-4 NB = 31.0507 1-4 EEL = 943.8597 VDWAALS =
-867.8167
EELEC = -3795.8614 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 274.2977 VIRIAL = 221.0695 VOLUME =
23770.5696
Density =
0.9657
Ewald error estimate: 0.7211E-05
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 2630000 TIME(PS) = 6099.000 TEMP(K) = 298.11 PRESS =
-386.9
Etot = -0.7332 EKtot = 2006.4763 EPtot =
-2007.2095
BOND = 702.2222 ANGLE = 840.0861 DIHED =
172.4913
1-4 NB = 32.0807 1-4 EEL = 947.7546 VDWAALS =
-856.6265
EELEC = -3845.2180 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 286.7887 VIRIAL = 487.2327 VOLUME =
23993.6284
Density =
0.9568
Ewald error estimate: 0.3826E-03
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 3690000 TIME(PS) = 7159.000 TEMP(K) = 289.31 PRESS =
-410.1
Etot = -32.5301 EKtot = 1947.2158 EPtot =
-1979.7459
BOND = 693.4976 ANGLE = 874.0986 DIHED =
159.6560
1-4 NB = 31.1085 1-4 EEL = 945.7069 VDWAALS =
-875.4696
EELEC = -3808.3440 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 277.1494 VIRIAL = 488.7902 VOLUME =
23901.8075
Density =
0.9604
Ewald error estimate: 0.6052E-04
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 2625000 TIME(PS) = 6094.000 TEMP(K) = 296.90 PRESS =
-27.0
Etot = 34.0073 EKtot = 1998.2983 EPtot =
-1964.2910
BOND = 697.5992 ANGLE = 880.4218 DIHED =
158.5524
1-4 NB = 33.1521 1-4 EEL = 940.4927 VDWAALS =
-867.2777
EELEC = -3807.2316 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 314.1616 VIRIAL = 328.0140 VOLUME =
23744.3305
Density =
0.9668
Ewald error estimate: 0.1166E-03
------------------------------------------------------------------------------
NSTEP = 3695000 TIME(PS) = 7164.000 TEMP(K) = 297.65 PRESS =
329.1
Etot = 43.7775 EKtot = 2003.3667 EPtot =
-1959.5891
BOND = 672.0363 ANGLE = 850.9861 DIHED =
158.0677
1-4 NB = 31.6230 1-4 EEL = 945.8010 VDWAALS =
-825.6377
EELEC = -3792.4656 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 276.7705 VIRIAL = 105.3118 VOLUME =
24130.3386
Density =
0.9514
Ewald error estimate: 0.1330E-03
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 3690000 TIME(PS) = 7159.000 TEMP(K) = 302.24 PRESS =
-643.0
Etot = 37.8007 EKtot = 2034.2591 EPtot =
-1996.4585
BOND = 694.5987 ANGLE = 894.6445 DIHED =
167.7689
1-4 NB = 33.7449 1-4 EEL = 946.0243 VDWAALS =
-906.2344
EELEC = -3827.0053 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 261.8648 VIRIAL = 590.4567 VOLUME =
23669.1351
Density =
0.9699
Ewald error estimate: 0.4195E-03
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 2635000 TIME(PS) = 6104.000 TEMP(K) = 297.98 PRESS =
-23.7
Etot = 85.3749 EKtot = 2005.6072 EPtot =
-1920.2323
BOND = 728.2609 ANGLE = 892.3597 DIHED =
171.3234
1-4 NB = 27.5064 1-4 EEL = 941.9280 VDWAALS =
-847.8771
EELEC = -3833.7335 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 288.5907 VIRIAL = 300.8125 VOLUME =
23833.7161
Density =
0.9632
Ewald error estimate: 0.7326E-04
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 3685000 TIME(PS) = 7154.000 TEMP(K) = 297.00 PRESS =
292.6
Etot = -9.6849 EKtot = 1999.0225 EPtot =
-2008.7074
BOND = 683.8339 ANGLE = 835.5606 DIHED =
174.1231
1-4 NB = 30.6777 1-4 EEL = 944.1515 VDWAALS =
-840.4570
EELEC = -3836.5971 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 302.1168 VIRIAL = 151.6776 VOLUME =
23813.0015
Density =
0.9640
Ewald error estimate: 0.1089E-03
------------------------------------------------------------------------------
NSTEP = 3695000 TIME(PS) = 7164.000 TEMP(K) = 293.86 PRESS =
296.7
Etot = 58.8247 EKtot = 1977.8261 EPtot =
-1919.0014
BOND = 709.9103 ANGLE = 889.1658 DIHED =
161.2241
1-4 NB = 32.2154 1-4 EEL = 945.8732 VDWAALS =
-854.1362
EELEC = -3803.2540 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 267.2744 VIRIAL = 114.2556 VOLUME =
23883.2202
Density =
0.9612
Ewald error estimate: 0.5591E-04
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 2635000 TIME(PS) = 6104.000 TEMP(K) = 290.32 PRESS =
767.8
Etot = -30.7424 EKtot = 1954.0485 EPtot =
-1984.7908
BOND = 687.4552 ANGLE = 890.5894 DIHED =
160.4413
1-4 NB = 33.5653 1-4 EEL = 943.9379 VDWAALS =
-826.9022
EELEC = -3873.8777 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 266.5895 VIRIAL = -122.0822 VOLUME =
23445.5175
Density =
0.9791
Ewald error estimate: 0.6461E-04
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 2625000 TIME(PS) = 6094.000 TEMP(K) = 299.26 PRESS =
-182.2
Etot = 26.8157 EKtot = 2014.2287 EPtot =
-1987.4130
BOND = 695.3858 ANGLE = 878.8070 DIHED =
163.1374
1-4 NB = 34.6737 1-4 EEL = 942.3073 VDWAALS =
-859.5041
EELEC = -3842.2201 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 281.3767 VIRIAL = 374.5347 VOLUME =
23676.3358
Density =
0.9696
Ewald error estimate: 0.2053E-03
------------------------------------------------------------------------------
tail: md2.out: file truncated
tail: md2.out: file truncated
NSTEP = 3680000 TIME(PS) = 7149.000 TEMP(K) = 296.08 PRESS =
-250.4
Etot = -35.7838 EKtot = 1992.7994 EPtot =
-2028.5832
BOND = 695.8828 ANGLE = 859.8540 DIHED =
173.8004
1-4 NB = 33.5450 1-4 EEL = 942.0584 VDWAALS =
-856.6877
EELEC = -3877.0361 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 276.0516 VIRIAL = 403.4121 VOLUME =
23557.4759
Density =
0.9745
Ewald error estimate: 0.1793E-03
------------------------------------------------------------------------------
NSTEP = 3695000 TIME(PS) = 7164.000 TEMP(K) = 300.38 PRESS =
303.2
Etot = 68.5983 EKtot = 2021.7294 EPtot =
-1953.1311
BOND = 686.3690 ANGLE = 854.5066 DIHED =
165.2733
1-4 NB = 30.6106 1-4 EEL = 941.9995 VDWAALS =
-855.2171
EELEC = -3776.6730 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 287.4091 VIRIAL = 132.9233 VOLUME =
23597.9182
Density =
0.9728
Ewald error estimate: 0.8944E-04
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 2640000 TIME(PS) = 6109.000 TEMP(K) = 297.90 PRESS =
-161.1
Etot = 56.5746 EKtot = 2005.0178 EPtot =
-1948.4433
BOND = 679.6320 ANGLE = 871.1519 DIHED =
166.2764
1-4 NB = 29.0489 1-4 EEL = 942.8578 VDWAALS =
-857.1475
EELEC = -3780.2628 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 284.0495 VIRIAL = 367.2160 VOLUME =
23905.0777
Density =
0.9603
Ewald error estimate: 0.3141E-03
------------------------------------------------------------------------------
tail: md2.out: file truncated
89.1
Etot = 8.9826 EKtot = 2029.4225 EPtot =
-2020.4399
BOND = 653.8919 ANGLE = 865.7852 DIHED =
157.6786
1-4 NB = 29.9679 1-4 EEL = 944.5274 VDWAALS =
-853.7606
EELEC = -3818.5304 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 288.1838 VIRIAL = 334.2048 VOLUME =
23909.0673
Density =
0.9602
Ewald error estimate: 0.1434E-03
------------------------------------------------------------------------------
NSTEP = 3695000 TIME(PS) = 7164.000 TEMP(K) = 302.00 PRESS =
243.0
Etot = 79.2729 EKtot = 2032.6757 EPtot =
-1953.4028
BOND = 727.2715 ANGLE = 853.7609 DIHED =
180.0856
1-4 NB = 30.4538 1-4 EEL = 943.1647 VDWAALS =
-806.9313
EELEC = -3881.2079 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 295.1073 VIRIAL = 170.2660 VOLUME =
23797.2861
Density =
0.9647
Ewald error estimate: 0.2139E-03
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 3700000 TIME(PS) = 7169.000 TEMP(K) = 293.75 PRESS =
-235.3
Etot = 19.9393 EKtot = 1977.1019 EPtot =
-1957.1627
BOND = 699.6437 ANGLE = 885.1597 DIHED =
160.6204
1-4 NB = 29.6013 1-4 EEL = 949.6956 VDWAALS =
-851.6958
EELEC = -3830.1876 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 278.3981 VIRIAL = 400.5057 VOLUME =
24031.5328
Density =
0.9553
Ewald error estimate: 0.8341E-05
------------------------------------------------------------------------------
tail: md2.out: file truncated
15.2
Etot = 42.3837 EKtot = 1996.4225 EPtot =
-1954.0389
BOND = 706.0816 ANGLE = 866.9725 DIHED =
173.1197
1-4 NB = 28.0721 1-4 EEL = 944.0886 VDWAALS =
-841.7418
EELEC = -3830.6316 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 272.3979 VIRIAL = 213.1446 VOLUME =
23830.5765
Density =
0.9633
Ewald error estimate: 0.2117E-03
------------------------------------------------------------------------------
NSTEP = 3695000 TIME(PS) = 7164.000 TEMP(K) = 292.74 PRESS =
-183.4
Etot = -33.2810 EKtot = 1970.3091 EPtot =
-2003.5902
BOND = 698.7424 ANGLE = 861.7805 DIHED =
176.4017
1-4 NB = 32.9699 1-4 EEL = 941.8824 VDWAALS =
-833.8322
EELEC = -3881.5348 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 277.1537 VIRIAL = 370.9414 VOLUME =
23679.0823
Density =
0.9695
Ewald error estimate: 0.2404E-03
------------------------------------------------------------------------------
tail: md2.out: file truncated
89.1
Etot = 8.9826 EKtot = 2029.4225 EPtot =
-2020.4399
BOND = 653.8919 ANGLE = 865.7852 DIHED =
157.6786
1-4 NB = 29.9679 1-4 EEL = 944.5274 VDWAALS =
-853.7606
EELEC = -3818.5304 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 288.1838 VIRIAL = 334.2048 VOLUME =
23909.0673
Density =
0.9602
Ewald error estimate: 0.1434E-03
------------------------------------------------------------------------------
NSTEP = 3700000 TIME(PS) = 7169.000 TEMP(K) = 292.85 PRESS =
-34.0
Etot = 7.7414 EKtot = 1971.0505 EPtot =
-1963.3091
BOND = 691.5552 ANGLE = 863.3626 DIHED =
151.5984
1-4 NB = 29.7049 1-4 EEL = 948.4176 VDWAALS =
-835.3891
EELEC = -3812.5588 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 286.2463 VIRIAL = 303.9691 VOLUME =
24116.3358
Density =
0.9519
Ewald error estimate: 0.9117E-04
------------------------------------------------------------------------------
tail: md2.out: file truncated
NSTEP = 3695000 TIME(PS) = 7164.000 TEMP(K) = 295.20 PRESS =
-125.0
Etot = 10.2777 EKtot = 1986.8564 EPtot =
-1976.5786
BOND = 689.8131 ANGLE = 857.3082 DIHED =
159.1225
1-4 NB = 24.3755 1-4 EEL = 944.2019 VDWAALS =
-856.7162
EELEC = -3794.6836 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 276.5899 VIRIAL = 341.1099 VOLUME =
23898.9516
Density =
0.9606
Ewald error estimate: 0.2683E-03
------------------------------------------------------------------------------
===============================================================
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Received on Wed Jan 22 2014 - 23:00:02 PST
