From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Jun 25 2012 - 00:37:43 CDT
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
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