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

From: Luthur Cheung (luthur_at_jhu.edu)
Date: Wed Jun 06 2012 - 10:27:58 CDT

Thanks for the reply. Let me try to slow down the pulling velocity and
see how it goes.

On 6/6/2012 10:21 AM, johan strumpfer wrote:
> Ajasja is right, this does indeed sound like hydrodynamic drag. You're
> pulling at 100 A / ns - pretty fast. Have a look at: Hsin& Schulten.
> Biophys. J. Letters 2011. You want to get to 1 A / ns or less, or
> close to that as you can afford.
>
> Cheers,
> Johan
>
> ------------------------------------------------------------------------------------------------------
> Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr
> Ph.D. Candidate
> Theoretical and Computational Biophysics Group
> 3115 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801, USA
> ------------------------------------------------------------------------------------------------------
>
>
> On Wed, Jun 6, 2012 at 9:47 AM, Ajasja Ljubetič
> <ajasja.ljubetic_at_gmail.com> wrote:
>> 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,
>> Ajasja
>>
>>
>> On 6 June 2012 15:31, Luthur Cheung<luthur_at_jhu.edu> 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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