Re: SMD output : which col represents force, second or last

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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