Re: SMD working only at high velocity

From: David Tanner (guacamoleo_at_gmail.com)
Date: Fri Jul 10 2009 - 15:20:23 CDT

The NAMD User's Guide explains how SMD moves an imaginary bead along
at a constant velocity; that bead is connected by a spring to your
atoms' center of mass. So, on average, you atoms will move along at a
constant velocity, but they are also free to move while attached to
the spring and imaginary bead.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.linkedin.com/in/davidetanner
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Jul 10, 2009, at 2:48 PM, Elia Zumot wrote:

Thanks for the response

It seems to be just fluctuating (back and forth) both in terms of the
position of COM along the direction of pulling and the force applied. It
doesn't much sense.

In any case isn't the whole idea of "constant velocity" SMD that
velocity
should be kept constant no matter whatever else happens?

Below is a sample of what I got when SMDk was 7 and 14:

Force is simply along the z= -1.0 axis

Info: SMD K 7
SMDTITLE: TS CURRENT_POSITION FORCE
SMD 100000 1.28943 1.57053 2.29581 0 0 -291.808
SMD 100020 1.30492 1.60175 2.28084 0 0 -284.586
SMD 100040 1.30695 1.6309 2.26294 0 0 -275.939
SMD 100060 1.30532 1.64695 2.24383 0 0 -266.703
SMD 100080 1.29978 1.64964 2.21972 0 0 -255.035
SMD 100100 1.28342 1.63699 2.19413 0 0 -242.645

SMD 105000 1.17835 1.66662 1.96988 0 0 -147.882
SMD 105020 1.17674 1.68279 1.92737 0 0 -127.266
SMD 105040 1.18771 1.69926 1.90175 0 0 -114.861
SMD 105060 1.21622 1.71099 1.88486 0 0 -106.706
SMD 105080 1.25246 1.72318 1.87483 0 0 -101.887
SMD 105100 1.28299 1.73917 1.86606 0 0 -97.6802

SMD 110000 1.38433 1.85559 2.04282 0 0 -197.945
SMD 110020 1.33297 1.87726 2.05002 0 0 -201.506
SMD 110040 1.27778 1.88458 2.05865 0 0 -205.763
SMD 110060 1.2292 1.8778 2.06142 0 0 -207.167
SMD 110080 1.20114 1.86165 2.06044 0 0 -206.752
SMD 110100 1.18436 1.83932 2.04681 0 0 -200.178

Info: SMD K 14
SMDTITLE: TS CURRENT_POSITION FORCE
SMD 100000 1.28943 1.57053 2.29581 0 0 -583.616
SMD 100020 1.30492 1.60174 2.27954 0 0 -567.905
SMD 100040 1.30597 1.63062 2.25847 0 0 -547.527
SMD 100060 1.30258 1.64659 2.23492 0 0 -524.739
SMD 100080 1.296 1.64846 2.20432 0 0 -495.086
SMD 100100 1.27729 1.63433 2.17151 0 0 -463.288

SMD 105000 1.46111 1.5459 1.82367 0 0 -153.545
SMD 105020 1.45561 1.55375 1.84524 0 0 -174.637
SMD 105040 1.44421 1.55863 1.85574 0 0 -184.974
SMD 105060 1.42889 1.56244 1.85736 0 0 -186.66
SMD 105080 1.41115 1.57235 1.84126 0 0 -171.119
SMD 105100 1.38526 1.58821 1.81888 0 0 -149.472

SMD 110000 1.16801 1.61488 1.95747 0 0 -312.869
SMD 110020 1.19037 1.62174 1.918 0 0 -274.601
SMD 110040 1.21714 1.63606 1.88775 0 0 -245.291
SMD 110060 1.24329 1.65345 1.86471 0 0 -222.994
SMD 110080 1.25918 1.67296 1.84001 0 0 -199.085
SMD 110100 1.26416 1.68962 1.81582 0 0 -175.672

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