Re: SMD output

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Thu Jan 22 2009 - 11:36:35 CST

It should be the force at that time t where the center of pulling is at
coords x, y, z.

C.

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Thu, Jan 15, 2009 at 4:50 PM, Dmitry Lupyan <dmitry.lupyan_at_mssm.edu>wrote:
> Hello namd-l,
>
> When i set "SMDOutputFreq 10" the output gives me this:
>
> SMD  10 5.72176 -3.38898 -0.00505686 -0 -0 -29.0444
> SMD  20 5.72647 -3.39013 -0.0134716 -0 -0 -23.1006
> SMD  30 5.70791 -3.44771 -0.0340012 -0 -0 -8.73964
> SMD  40 5.68444 -3.47025 -0.0349437 -0 -0 -7.98754
> SMD  50 5.6734 -3.48958 -0.0478025 0 0 1.04392
> SMD  60 5.67285 -3.52725 -0.010169 -0 -0 -25.0062
> SMD  70 5.68524 -3.517 0.0260181 -0 -0 -50.0513
> SMD  80 5.67241 -3.53038 0.0340123 -0 -0 -55.5083
> SMD  90 5.68427 -3.55666 0.0417895 -0 -0 -60.8146
> SMD  100 5.70028 -3.52214 0.0322488 -0 -0 -54.0885
>
> the force in this output is the instantaneous force at step
> 10,20,30,etc... or the average of the 10 steps?
>
> thanks
> -dima
>
>
-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078

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