From: Hyuntae Na (htna_at_hotmail.com)
Date: Fri Jun 22 2012 - 19:56:14 CDT
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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