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

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Aug 05 2009 - 13:10:34 CDT

Force is in the last three columns. At the beginning of the log you will
see a line:

SMDTITLE: TS CURRENT_POSITION FORCE

Force is not just a number, it's a vector. That's why you can have
negative numbers. If you want to calculate the magnitude of the force you
have to calculate the length of the force vector:

     F = sqrt (Fx^2 + Fy^2 + Fz^2)

Fx, Fy and Fz are the three components of the force vector.

Gianluca

On Wed, 5 Aug 2009, snoze pa 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
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     +1 (206) 714 4303
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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