From: Hyuntae Na (htna_at_hotmail.com)
Date: Mon Jun 25 2012 - 00:59:18 CDT
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 GPRESSAVGENERGY: 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
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:42 CST