From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Tue May 29 2007 - 16:45:17 CDT
Thanks for the link and for the suggestion. I will give it a try.
JC Gumbart escribió:
> It's nearly impossible to reproduce the exact same numbers, even when
> things should be deterministic, because of the limits of computational
> accuracy.
>
> Jim mentions this here:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1317.html
>
> As for your other issue, it's not clear to me either why the jump in
> energy would occur. You should be able to use NAMD energy in VMD to
> compute the energy for selected parts of the system to try to narrow
> down where it's occurring, perhaps a single residue even. That would
> help a lot.
>
> On May 29, 2007, at 3:51 PM, Cesar Luis Avila wrote:
>
>> As I previously pointed out KINETIC, and as a consequence
>> TEMPERATURE, along with ANGLE and DIHED experiment this shift. I also
>> monitored protein backbone rmsd but nothing strange happens on that
>> period. A visual inspection on the trajectory does not reveal
>> anything strange either. I have restarted a new simulation from 10ns
>> saving the frames and energy every ps. But for the first 10 ps the
>> energy reported is different even though I have used the same seed.
>>
>> hl332_at_drexel.edu escribió:
>>> It all sounds right. Have you seen anything weird in your system
>>> between these time steps when energy shows a sudden increase? What
>>> happens to temperature in this range? yes, i understand one week is
>>> pretty long time to redo the run.
>>>
>>> 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: Tuesday, May 29, 2007 10:53 am
>>> Subject: Re: namd-l: Energy shift during simulation
>>>
>>>
>>>> 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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