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

From: johan strumpfer (
Date: Wed Jun 06 2012 - 09:21:23 CDT

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.


Johan Strumpfer:
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 Ljubeti~M
<> 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 <> 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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