From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Tue May 29 2007 - 09:53:31 CDT
The restart files, time step and seed are exactly the same as those from
previous runs. Indeed the shift appears in the middle of the run, not at
restart. "1ns" takes a week on my small cluster :(. Since it is the
first time that i see something like this, I do not know if this shift
might be regarded as normal, or if it should be recalculated.
Attached I send you a snapshot of the TOTAL energy plot vs timestep.
Please ask for any other graph or data needed to work this out.
Thanks for your help.
Cesar
hl332_at_drexel.edu escribió:
> Check again and make sure, you did take the right restart files, right time step from end of previous run and right seed. If still not convinced, try restarting run for this "1ns" period again which wont take too long. Thats what I would do in case unable to find reason of why this shift?
>
> Harish
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823
>
> ----- Original Message -----
> From: Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>
> Date: Monday, May 28, 2007 7:26 pm
> Subject: Re: namd-l: Energy shift during simulation
>
>
>> I have the TOTAL energy fluctuating around a given value for nearly
>> 10
>> ns. At 10.5 ns I suddenly observe a shift in the energy as well as
>> in
>> the temperature and then it returns to previous values at 11 ns.
>> I am aware that the energy won't be fixed, but this sudden shift
>> seems
>> suspicious.
>>
>> hl332_at_drexel.edu escribió:
>>
>>> Hi,
>>> You have been using an NPT ensemble run where number of
>>>
>> particles, pressure, temperature should stay constant and Energy is
>> variable. I dont see what the problem is really? If you want to
>> make energy constant, do an NVE run instead.
>>
>>> I hope it helps.
>>>
>>> Harish
>>>
>>>
>>> -------------------------------------------------
>>> Harish Vashisth (Ph.D Candidate)
>>> CAT-361,Chemical & Biological Engg.
>>> Drexel University, Philadelphia, PA
>>> office: 215-895-5823
>>>
>>> ----- Original Message -----
>>> From: Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>
>>> Date: Monday, May 28, 2007 5:21 pm
>>> Subject: namd-l: Energy shift during simulation
>>>
>>>
>>>
>>>> Dear all,
>>>> I am conducting a simulation of a protein membrane system. I
>>>>
>> have
>>
>>>> decided to split the simulation on 1 ns step, saving energies
>>>>
>> and
>>
>>>> coordinates every 10 ps. I am using NPT ensemble (Langevin)
>>>>
>> using
>>
>>>> ConstantRatio.
>>>>
>>>> After 10 ns I noticed a shift on the TOTAL energy (contributed
>>>> mainly by
>>>> ANGLE + DIHEDRAL + KINETIC ) and TEMP around step 10420000. The
>>>> ENERGY
>>>> returns to previous values only when I restarted the simulation
>>>>
>> on
>>
>>>> step
>>>> 11000000.
>>>>
>>>> Any clue on what might be happening? And what should I do?
>>>>
>> Discard
>>
>>>> this
>>>> data and resume from step 100000?
>>>>
>>>> ETITLE: TS BOND ANGLE DIHED
>>>>
>>
>>
>>>>
>>>> IMPRP ELECT VDW BOUNDARY
>>>>
>>>> MISC KINETIC TOTAL TEMP
>>>> TOTAL2 TOTAL3 TEMPAVG PRESSURE
>>>> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>>>>
>>>> ENERGY: 10300000 63609.6505 64570.8779 16318.2654
>>>>
>>
>>
>>>> 917.3728 -591430.8385 29709.2435 0.0000
>>>>
>>
>>
>>>> 0.0000 185866.1012 -230439.3271 324.1665
>>>> -228060.7668 -227954.7134 325.0299 1450.5216
>>>>
>>
>>
>>>> -197.6874 1853385.2552 0.0403 -0.1946
>>>> ENERGY: 10310000 63800.1438 64113.9093 16373.1687
>>>>
>>
>>
>>>> 904.6770 -591969.1599 29918.4770 0.0000
>>>>
>>
>>
>>>> 0.0000 185952.7454 -230906.0388 324.3176
>>>> -228503.6012 -228511.4695 325.0235 1680.2639
>>>>
>>
>>
>>>> -79.4904 1850572.7046 1.5285 1.8823
>>>> ENERGY: 10320000 63731.1341 64542.3796 16312.3888
>>>>
>>
>>
>>>> 928.3302 -592395.1306 29677.3780 0.0000
>>>>
>>
>>
>>>> 0.0000 186575.9104 -230627.6093 325.4044
>>>> -228229.7364 -228220.0970 325.0447 1684.6130
>>>>
>>
>>
>>>>
>>>> 19.3906 1847303.2782 1.0025 1.0650
>>>> ENERGY: 10330000 63398.1087 64145.3713 16404.7305
>>>>
>>
>>
>>>> 931.7793 -592090.6118 29817.9364 0.0000
>>>>
>>
>>
>>>> 0.0000 186508.3964 -230884.2891 325.2867
>>>> -228503.4313 -228433.2293 325.0251 1733.0630
>>>>
>>
>>
>>>> -189.9830 1848356.1095 1.7627 1.7452
>>>> ENERGY: 10340000 63918.9096 64585.9508 16418.7835
>>>>
>>
>>
>>>> 875.5280 -592955.6394 30736.1507 0.0000
>>>>
>>
>>
>>>> 0.0000 186098.4177 -230321.8992 324.5717
>>>> -227926.7176 -227884.4924 325.0322 2101.0069
>>>>
>>
>>
>>>> 229.6281 1851654.4936 1.4528 1.6165
>>>> ENERGY: 10350000 63567.5613 64759.4829 16217.4356
>>>>
>>
>>
>>>> 889.1424 -591727.6567 29738.3133 0.0000
>>>>
>>
>>
>>>> 0.0000 186278.3960 -230277.3253 324.8856
>>>> -227879.1186 -227873.0291 325.0988 1914.3131
>>>>
>>
>>
>>>>
>>>> 95.1531 1850918.0950 0.0627 0.0207
>>>> ENERGY: 10360000 63901.9471 64255.2030 16386.2734
>>>>
>>
>>
>>>> 925.6849 -591209.3716 29854.6413 0.0000
>>>>
>>
>>
>>>> 0.0000 186425.9808 -229459.6412 325.1430
>>>> -227064.1050 -227027.4999 325.0474 1777.5875
>>>>
>>
>>
>>>> -50.7852 1852831.2636 -0.3381 -1.0205
>>>> ENERGY: 10370000 63339.7705 64689.0525 16414.3804
>>>>
>>
>>
>>>> 909.3640 -592508.3969 30184.9106 0.0000
>>>>
>>
>>
>>>> 0.0000 186440.8797 -230530.0392 325.1689
>>>> -228121.7505 -228155.9220 325.0388 1907.0434
>>>>
>>
>>
>>>>
>>>> -4.1627 1850041.9880 0.2329 0.4851
>>>> ENERGY: 10380000 63178.1926 64696.6552 16347.7512
>>>>
>>
>>
>>>> 939.7491 -591640.3336 29881.3682 0.0000
>>>>
>>
>>
>>>> 0.0000 186839.2189 -229757.3984 325.8637
>>>> -227369.7937 -227323.4315 325.0963 1977.5063
>>>>
>>
>>
>>>> -30.4046 1847092.7663 -0.5036 -0.7161
>>>> ENERGY: 10390000 63996.0173 64648.3814 16396.8117
>>>>
>>
>>
>>>> 926.3078 -592074.6561 30166.7425 0.0000
>>>>
>>
>>
>>>> 0.0000 185975.2774 -229965.1180 324.3569
>>>> -227577.4960 -227516.0743 325.0763 1905.7479
>>>>
>>
>>
>>>>
>>>> 93.6511 1849921.5963 0.9937 0.8142
>>>> ENERGY: 10400000 63853.9013 64070.7798 16331.7615
>>>>
>>
>>
>>>> 924.0796 -591846.8154 30145.9941 0.0000
>>>>
>>
>>
>>>> 0.0000 186696.5286 -229823.7704 325.6148
>>>> -227428.0385 -227387.5511 325.0728 1747.0664
>>>>
>>
>>
>>>>
>>>> 28.2482 1854110.4170 -2.8355 -2.2988
>>>> ENERGY: 10410000 63488.3269 64647.3090 16436.2537
>>>>
>>
>>
>>>> 921.6758 -591827.7839 30088.6061 0.0000
>>>>
>>
>>
>>>> 0.0000 186010.3933 -230235.2190 324.4181
>>>> -227840.1402 -227818.6152 324.9854 1820.6818
>>>>
>>
>>
>>>> -27.9187 1849769.2296 -0.4637 0.1865
>>>> ENERGY: 10420000 63778.0021 64998.8286 16599.4685
>>>>
>>
>>
>>>> 924.7329 -591598.4523 29967.0566 0.0000
>>>>
>>
>>
>>>> 0.0000 187299.0044 -228031.3592 326.6656
>>>> -225627.9244 -225593.2967 326.2422 1803.6118
>>>>
>>
>>
>>>> -110.9619 1850160.6637 1.7969 1.8479
>>>> ENERGY: 10430000 64008.6044 65556.9899 16769.9379
>>>>
>>
>>
>>>> 927.1032 -591933.4968 30377.2170 0.0000
>>>>
>>
>>
>>>> 0.0000 187947.0020 -226346.6424 327.7957
>>>> -223936.7567 -223933.8235 327.1259 1956.7638
>>>>
>>
>>
>>>> -35.1648 1851146.0456 2.3698 2.3364
>>>> ENERGY: 10440000 63967.3836 65310.1901 16548.3853
>>>>
>>
>>
>>>> 876.5539 -592244.7863 30355.2727 0.0000
>>>>
>>
>>
>>>> 0.0000 186854.5382 -228332.4625 325.8904
>>>> -225906.7514 -225967.7844 327.1985 1851.4702
>>>>
>>
>>
>>>>
>>>> 67.3314 1851539.2548 0.1672 0.1645
>>>> ENERGY: 10450000 64043.4908 65300.3392 16628.0304
>>>>
>>
>>
>>>> 911.8170 -591921.1518 30147.7787 0.0000
>>>>
>>
>>
>>>> 0.0000 187477.2339 -227412.4619 326.9764
>>>> -224980.4613 -225036.7252 327.0621 1954.6794
>>>>
>>
>>
>>>>
>>>> 81.8472 1851476.2295 2.8552 2.8622
>>>> ENERGY: 10460000 63831.1771 65127.2486 16578.3829
>>>>
>>
>>
>>>> 890.9648 -592695.3985 30367.5321 0.0000
>>>>
>>
>>
>>>> 0.0000 187176.1816 -228723.9114 326.4514
>>>> -226330.8714 -226248.8746 326.9795 1969.0847
>>>>
>>
>>
>>>>
>>>> 19.2833 1849709.6477 1.2673 1.2717
>>>> ENERGY: 10470000 63931.1120 65583.6408 16413.7982
>>>>
>>
>>
>>>> 941.7629 -592226.2966 30156.8957 0.0000
>>>>
>>
>>
>>>> 0.0000 188021.6487 -227177.4382 327.9259
>>>> -224798.4522 -224667.5801 327.0829 1832.2226
>>>>
>>
>>
>>>> -19.2946 1851583.0035 0.2917 0.6956
>>>> ENERGY: 10480000 63687.5879 65078.5959 16564.2646
>>>>
>>
>>
>>>> 918.0522 -591566.5008 30384.6587 0.0000
>>>>
>>
>>
>>>> 0.0000 186963.3201 -227970.0215 326.0801
>>>> -225542.0302 -225593.2482 326.8874 1800.6804
>>>>
>>
>>
>>>> -23.3607 1852368.2878 -2.5195 -2.0388
>>>> ENERGY: 10490000 64074.4914 64860.3827 16618.2216
>>>>
>>
>>
>>>> 921.0558 -593361.4120 30875.6371 0.0000
>>>>
>>
>>
>>>> 0.0000 187303.2910 -228708.3325 326.6731
>>>> -226298.1552 -226282.6418 326.8636 1730.4118
>>>>
>>
>>
>>>> -49.5610 1852771.6838 -1.5235 -1.2356
>>>> ENERGY: 10500000 63640.9008 65012.5143 16530.3874
>>>>
>>
>>
>>>> 916.0746 -592011.6342 30193.3293 0.0000
>>>>
>>
>>
>>>> 0.0000 187557.1582 -228161.2696 327.1158
>>>> -225738.1892 -225772.5514 326.9812 2056.2349
>>>>
>>
>>
>>>>
>>>> 52.2942 1851763.0133 0.7401 0.4435
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>
>
>
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