From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Wed Aug 05 2009 - 12:05:16 CDT
SMD line format:
SMD timestep x y z fx fy fz
keep in mind that SMD reads the initial position of the pulled atom
from pdb file indicated in SMD lines of namd config file.
On Wed, Aug 5, 2009 at 12:25 PM, snoze pa<snoze.pa_at_gmail.com> wrote:
> Dear NAMD users,
>
> I have a question related to SMD output. In the tutorials, I have
> following output
>
> PRESSURE: 19900 0 0 0 0 0 0 0 0 0
> GPRESSURE: 19900 0 0 0 0 0 0 0 0 0
> PRESSAVG: 19900 0 0 0 0 0 0 0 0 0
> GPRESSAVG: 19900 0 0 0 0 0 0 0 0 0
> ENERGY: 19900 432.2630 1310.0679 494.0138
> 91.9899 -2226.3118 -9.8910 0.0000
> 0.0000 1956.2369 2048.3687 643.2036
> 2071.2116
> 2070.9957 637.6917
>
> SMD 19910 69.8912 78.0177 116.999 424.611 484.495 1018.15
> SMD 19920 69.8791 77.9465 116.957 444.918 507.667 1066.84
> SMD 19930 69.8716 77.9768 116.959 451.504 515.181 1082.64
> SMD 19940 69.6606 78.0433 116.932 472.194 538.789 1132.25
> SMD 19950 69.4807 78.0557 117.034 475.988 543.118 1141.34
> SMD 19960 69.4138 78.0986 117.173 465.485 531.133 1116.16
> SMD 19970 69.3529 78.1149 117.211 471.105 537.547 1129.64
> SMD 19980 69.3644 78.1475 117.155 484.875 553.258 1162.65
> SMD 19990 69.3612 78.1582 117.214 484.352 552.662 1161.4
> SMDTITLE: TS CURRENT_POSITION FORCE
> SMD 20000 69.4411 78.2579 117.237 477.894 545.292 1145.91
>
>
> Which column represent force: Is it the last coulm? If it is last then
> why i am getting negative number in last col. My simulation is
> producing following results when I am unfolding a protein.
>
> PRESSURE: 153000 0 0 0 0 0 0 0 0 0
> GPRESSURE: 153000 0 0 0 0 0 0 0 0 0
> PRESSAVG: 153000 0 0 0 0 0 0 0 0 0
> GPRESSAVG: 153000 0 0 0 0 0 0 0 0 0
> TIMING: 153000 CPU: 3337.98, 0.0236324/step Wall: 4417.6,
> 0.0384204/step, 3.7033 hours remaining, 18.292038 MB of memory in use.
> ENERGY: 153000 290.3905 767.7847 446.2963
> 38.3142 -67996.4902 6000.2716 0.0000
> 0.0000 11676.6037 -48776.8292 303.2505
> -60453.4329 -48768.3205 303.4466
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 153000
> WRITING COORDINATES TO DCD FILE AT STEP 153000
> WRITING COORDINATES TO RESTART FILE AT STEP 153000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 153000
> FINISHED WRITING RESTART VELOCITIES
> SMD 153100 78.3199 -32.8057 -31.0879 934.363 -422.56 -321.49
> SMD 153200 78.2873 -32.6977 -31.2891 956.163 -432.419 -328.99
> SMD 153300 78.2761 -32.5069 -31.325 1000.73 -452.576 -344.326
> SMD 153400 78.3005 -32.3314 -31.3024 1038.32 -469.572 -357.257
> SMD 153500 78.2221 -32.3442 -31.4566 1062.4 -480.464 -365.544
> SMD 153600 78.2414 -32.4233 -31.4773 1060.92 -479.795 -365.035
> SMD 153700 78.4328 -32.6028 -31.4118 1000.76 -452.587 -344.335
> SMD 153800 78.3506 -32.6825 -31.4559 1028.43 -465.102 -353.856
> SMD 153900 78.4919 -32.8572 -31.3801 985.696 -445.775 -339.152
> SMD 154000 78.6241 -32.9805 -31.1638 968.179 -437.853 -333.125
>
>
> Thank you,
>
> S
>
>
-- Roman Petrenko Physics Department University of Cincinnati
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