From: tillmann.utesch_at_mail.tu-berlin.de
Date: Tue Jun 26 2012 - 03:03:34 CDT
Did you remove position restraints from your system after the minimization?
Quoting Hyuntae Na <htna_at_hotmail.com>:
>
> Hi, I agree that I should take longer minimization steps than 300. I
> tested the 20,000 minimization step. After its minimization
> iteration takes around 10,000 steps (the half of 20,000), the
> protein in the water box is almost reached to its minimum structure
> (its conformation does not change much except small fluctuation). By
> the way, after the minimization with 20,000 steps is fully done, the
> energy drop still exists. In this case, should the minimization be
> continued until there is no atom movement at all? One my question is
> if the MD simulation test example in the tutorial files,
> "namd-tutorial-files\1-3-box", runs with improper minimization,
> because its log also shows the same bond energy drop : 605.1437 ->
> 81.9360.
> Thank you very much. Best regards,--Hyuntae From:
> norman.geist_at_uni-greifswald.de
> To: htna_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
> Subject: AW: AW: namd-l: Sudden energy drop after minimization
> Date: Tue, 26 Jun 2012 08:40:39 +0200
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> "Regarding "300
> minimization step", I selected the number by comparing the energy and
> pressure variation between 100 - 2,000."
>
>
>
> I
> have no idea what you mean. If you minimize correctly there is no more
> variation in energies. And during minimization, there´s also no pressure
> variation as it is constant volume and no temperature. Also, if the
> system isn´t
> minimized correctly, there can be tensions in bonds and angles that
> unload with
> the start of the molecular dynamic and so transfer to kinetic energy.
>
>
>
> Arons
> suggestion also sounds a good idea to check.
>
>
>
>
>
> Norman Geist.
>
>
>
>
>
>
>
>
>
>
>
> Von:
> owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Hyuntae
> Na
>
> Gesendet: Montag, 25. Juni 2012 07:59
>
> An: norman.geist_at_uni-greifswald.de
>
> Cc: namd-l_at_ks.uiuc.edu
>
> Betreff: RE: AW: namd-l: Sudden energy drop after minimization
>
>
>
>
>
>
>
>
>
> Hi,
>
>
>
> Thank you for you comment. The same situation happens in VMD tutorial file
> too. If you look the log of "namd-tutorial-files\1-3-box",
> the bond energy was decreased heavily also.
>
>
>
> ==========================================
>
> LINE MINIMIZER BRACKET: DX 0.000711118 0.00142224 DU -15.5301 325.354 DUDX
> -101999 59282 403961
>
> PRESSURE: 100 -5584.57 -163.474 118.351 -163.474 -5545.59 104.068 118.351
> 104.068 -5585.23
>
> GPRESSURE: 100 -6177 -188.545 78.1791 -127.553 -6102.01 191.88
> 203.577 164.188
> -6078.77
>
> Info: Initial time: 4 CPUs 0.0346818 s/step 0.200705 days/ns 267.297
> MB memory
>
> ETITLE:
> TS BOND
> ANGLE
> DIHED
> IMPRP
> ELECT
> VDW
> BOUNDARY
> MISC KINETIC
> TOTAL
> TEMP
> POTENTIAL TOTAL3
> TEMPAVG
> PRESSURE
> GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 100
> 605.1437
> 733.6868
> 263.5997
> 11.0217
> -23673.7631
> 915.4026
> 0.0000
> 0.0000 0.0000
> -21144.9086
> 0.0000 -21144.9086
> -21144.9086
> 0.0000
> -5571.7963 -6119.2600
> 86856.0000 -5571.7963
> -6119.2600
>
>
>
> REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
>
> TCL: Running for 2500 steps
>
> PRESSURE: 100 -3391.8 -118.583 163.544 -118.583 -3457.46 240.736 163.544
> 240.736 -3391.52
>
> GPRESSURE: 100 -3448.04 -186.276 91.045 -110.856 -3363.57 137.289 193.572
> 124.827 -3334.27
>
> ENERGY: 100
> 81.9360
> 262.9427
> 263.6823
> 10.9727
> -21774.1928
> 893.5803
> 0.0000
> 0.0000 4500.6962
> -15760.3825 308.0595
> -20261.0787 -15770.7326
> 308.0595 -3413.5938
> -3381.9607 86856.0000
> -3413.5938 -3381.9607
>
> ==========================================
>
>
>
> As you see in the above capture, which is actually the copy from
> "namd-tutorial-files\1-3-box\example-output\ubq_wb_eq.log" in the
> tutorial files, the bond energy is decreased from 605.1437 to
> 81.9360. I am wondering if this is acceptable.
>
>
>
> Regarding "300 minimization step", I selected the number by comparing
> the energy and pressure variation between 100 - 2,000.
>
>
>
> Best regards,
>
> -- Hyuntae
>
>
>
>
>
>
>
>
>
>>
> From: norman.geist_at_uni-greifswald.de
>
>> To: htna_at_hotmail.com
>
>> CC: namd-l_at_ks.uiuc.edu
>
>> Subject: AW: namd-l: Sudden energy drop after minimization
>
>> Date: Mon, 25 Jun 2012 07:37:43 +0200
>
>>
>
>> Hi,
>
>>
>
>> as far as I can see, the total energy raised after minimization, what is
>
>> expectable because of introduction of temperature. The energy you
> mentioned
>
>> is the bonded energy, and was decreased heavily, but I'm sure that comes
> due
>
>> to your way to short minimization. From the energies and the step times, I
>
>> think you have a quit big system. Only 300 minimization steps is extremely
>
>> too short. You should plot your total energy to see when it get nearly
>
>> constant. Use the VMD namd plot plugin for that. I think an amount of
>
>> 10.000-50.000 steps minimization is what you need.
>
>>
>
>> Norman Geist.
>
>>
>
>> > -----Ursprüngliche Nachricht-----
>
>> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>
>> > Auftrag von Hyuntae Na
>
>> > Gesendet: Samstag, 23. Juni 2012 02:56
>
>> > An: namd-l_at_ks.uiuc.edu
>
>> > Betreff: namd-l: Sudden energy drop after minimization
>
>> >
>
>> >
>
>> > Hi All,
>
>> >
>
>> >
>
>> > I faced one not understable case while running MD simullation. I want
>
>> > to know if this is the known issue, or if there is a bug in my
>
>> > configuration.
>
>> >
>
>> >
>
>> > I set 300 iteration to minimize a protwin within a waterbox, and set
>
>> > 250000 iterations (500 ps) for the MD simulation. In the mean time,
>
>> > after the minimization step, the error drops drastically just before
>
>> > the MD simulation starts. Following is the capture of its log:
>
>> >
>
>> >
>
>> > ===============================================================
>
>> >
>
>> > LINE MINIMIZER BRACKET: DX 5.8119e-06 2.52175e-06 DU -0.0359273
>
>> > 0.0067846 DUDX -11927.6 102.202 5360.57
>
>> > LINE MINIMIZER REDUCING GRADIENT FROM 2.81013e+06 TO 2810.13
>
>> > PRESSURE: 300 -6445.5 41.062 130.819 41.062 -6200.95 -15.5486 130.819
> -
>
>> > 15.5486 -6405.64
>
>> > GPRESSURE: 300 -6275.61 83.2379 73.7774 72.8995 -6127.56 -41.0635
>
>> > 98.9947 8.3979 -6236.38
>
>> > Info: Benchmark time: 18 CPUs 0.913816 s/step 1057.66 days/ns 2548.52
>
>> > MB memory
>
>> > ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC
> TOTAL
>
>> > TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
>
>> > GPRESSAVG
>
>> >
>
>> > ENERGY: 300 7269.7257 6938.1628 3126.9451 85.7711 -260020.0382
>
>> > 11411.5320 0.0000 0.0000 0.0000 -231187.9015 0.0000 -231187.9015 -
>
>> > 231187.9015 0.0000 -6350.6979 -6213.1839 794942.8795 -6350.6979 -
>
>> > 6213.1839
>
>> >
>
>> > REINITIALIZING VELOCITIES AT STEP 300 TO 310 KELVIN.
>
>> > TCL: Running for 250000 steps
>
>> > PRESSURE: 300 -3030.49 98.8762 52.9485 98.8795 -2881.76 -44.5797
>
>> > 52.9495 -44.5823 -2989.42
>
>> > GPRESSURE: 300 -3011.47 97.7027 79.4894 74.7973 -2851.13 -62.2207
>
>> > 63.1423 -24.2313 -2948.84
>
>> > ENERGY: 300 546.5513 1998.3257 3126.8298 85.6771 -238049.2276
>
>> > 11143.8978 0.0000 0.0000 46586.0825 -174561.8635 309.2931
> -221147.9460
>
>> > -174561.8651 309.2931 -2967.2253 -2937.1491 794942.8795 -2967.2253 -
>
>> > 2937.1491
>
>> >
>
>> > ===============================================================
>
>> >
>
>> >
>
>> > The energy was 7269.7257, and temparature was 0.0000 just after the
>
>> > minimization finished.
>
>> >
>
>> > However, the energy dropped as 546.5513 while the temparature became
>
>> > 309.2931.
>
>> >
>
>> >
>
>> >
>
>> > I am wondering if this energy drop indicate the error of my
> structure,
>
>> > or not. I could observe the same situation in the NAMD tutorial
> "namd-
>
>> > tutorial-files/1-3-box" too.
>
>> >
>
>> >
>
>> >
>
>> > Thank you very much.
>
>> >
>
>> >
>
>> >
>
>> > Best regards,
>
>> >
>
>> > -- Hyuntae
>
>>
>
>
>
>
>
>
>
>
-- Tillmann Utesch Institut für Chemie, Max-Volmer-Laboratorium TU Berlin, PC 14 Straße des 17. Juni 135 D-10623 Berlin Tel. +49-(0)30-314-26389
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