Re: SMD working only at high velocity

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jul 10 2009 - 13:26:06 CDT

Are you sure it's "not working" or the force just hasn't built up
enough to unbind it? If you plot your SMD forces, I would guess that
they are increasing constantly when the ligand is not yet moving.
Try increasing your SMDk to see if that makes it happen quicker.

On Jul 10, 2009, at 1:20 PM, Elia Zumot wrote:

>
> Dear all,
>
> I'm attempting to move a substrate bound to the protein out of the
> binding
> pocket to see what conformational changes that induces (and major
> changes
> are expected in this case). I'm using SMD with constant velocity
> for that
> with certain harmonic constraints imposed on the protein backbone to
> prevent net translational movement.
>
> The problem is that the simulation only works at a velocity as 500
> A/ns
> but not at the more realistic velocities of 2 or 6 A/ns. This
> doesn't seem
> to make sense (at least not to me) since a lower velocity should
> mean a
> longer time but not a mere fluctuation of the substrate in its initial
> position (validated by the visualization of the trajectory in VMD
> and the
> position of COM along the direction of applied force).
>
> Am I missing something here?
>
> Thanks
>
> Elia
>
>

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