From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Fri Jul 10 2009 - 15:06:20 CDT
This really is far too short a sampling time to figure out what is
going on. You should be able to forcibly pull the protein out of the
binding pocket using CV SMD provided you have chosen the appropriate
reaction coordinate and simulated long enough to get the separation
distance you need to "detach" them. How deep is this binding pocket,
and how far do you want to the drug out? I would suggest a simulation
of at least several nanoseconds before giving up on a pulling velocity
which should give you the separation you need.
Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu
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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