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

From: Eric H. Lee (ericlee_at_illinois.edu)
Date: Wed Jun 06 2012 - 11:28:19 CDT

I agree with Johan. Some other factors to check out are whether your periodic box is large enough (to make sure you are not colliding with the mirror image), or the chance of local deformation to one of the pulled structures.

100A/ns is incredibly fast and you may want to repeat at a lower pulling velocity, but examine your current trajectory very carefully to figure out if pulling slower may capture some interactions which were observed but fleeting in your current trajectory.

Eric H. Lee, Ph.D.
Medical Scholars Program
Theoretical and Computational Biophysics Group
ericlee_at_ks.uiuc.edu

On Jun 6, 2012, at 9:21 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 Ljubeti─~M
> <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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