From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jun 26 2012 - 04:31:42 CDT
Please use VMD->Extensions->Analysis->NAMD plot with your outfile of the
minimization and watch if the total energy keeps still decreasing. The
minimization should continue till the total energy is absolute constant to
be save. (you will have to zoom as often very high initial peaks distort the
y axes scaling and the energy seems to be constant, but it isn't)
Also, there shouldn't be much atom movement during minimization in general.
And at the end, there should be absolutely no movement anymore.
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von tillmann.utesch_at_mail.tu-berlin.de
> Gesendet: Dienstag, 26. Juni 2012 10:04
> An: namd-l_at_ks.uiuc.edu
> Betreff: RE: AW: AW: namd-l: Sudden energy drop after minimization
>
> 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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