Re: pulling force didn't drop to zero in SMD

From: Ajasja Ljubetič (
Date: Wed Jun 06 2012 - 08:47:35 CDT

Disclamer: I have yet to perform a SMD pulling experiment.
But having said that, if this is not in vacuum, then the force could be due
to the viscosity of the medium (water)?

Best regads,

On 6 June 2012 15:31, Luthur Cheung <> wrote:

> Hi, I was using the SMD to unbind two proteins under a constant pulling
> velocity. I extracted the pulling force by following the "ft.tcl" script
> mentioned in the tutorial. At the beginning, the pulling force was fine and
> increased as one of the protein under pulling by the SMD atom. Later on,
> when these two proteins were separated, the pulling force started to slowly
> decrease. However, the value didn't drop to zero even though the two
> protein molecules were already far apart with each other.
> Let me put some numbers here in case that help for analyzing my problem:
> The pulling force will slowly decrease to ~1000 pN and stayed there
> Spring constant k is 1 to 4 kcal/mol/A^2
> Pulling velocity is 0.0001 to 0.00005 A/step
> Standard time step = 2 femtoseconds
> Does anyone know what causes the pulling force not decreasing to zero
> while the two proteins are already unbound? If it is necessary, I could
> also upload the force-time curve. Thanks!
> Best Regards,
> Luthur

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