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

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Aug 05 2009 - 13:34:15 CDT

Thank you very much to you all.

With Kind Regards

S

On Wed, Aug 5, 2009 at 1:10 PM, Gianluca
Interlandi<gianluca_at_u.washington.edu> wrote:
> 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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