[gmx-users] Pull Simulation: Force spike on F vs X output and extension stall

[Justin A. Lemkul]

Natalie Stephenson wrote:
> Hi,
> 
>  
> 
> I was wondering if you would be able to clear up a slightly confusing 
> aspect of the simulations I've been running. 
> 
>  
> 
> I am currently performing a pull simulation and when viewing the outputs 
> of all the simulations I have run I see the extension of the protein 
> stop when it reaches the same sub-domain each time (at around a 10 nm 
> extension).  The mdp file I use as the input file states that the pull 
> distance should be much larger than this.
> 
>  
> 
> Also when viewing the -px -pf outputs this agrees.  When the simulation 
> reaches a 10 nm extension it stops and only increases around 0.2 nm over 
> the remaining simulation time (~3000 ps). When force extension is 
> plotted there is still an increase in force which results in a spike at 
> the 10 nm extension point, increasing the force from around 0.7 nN to 
> around 30 nN. 
> 
>  
> 
> Is there any reason this could be an artefact or is it just the fact 
> that this domain is very firmly in contact with it's adjacent domain?
> 

Is your box of sufficient size?  Your pull distance must always be less than 
half the box vector in the pulling dimension (unless using the 
direction_periodic geometry, which may or may not be available in your Gromacs 
version, but you haven't said which you're using).  What type of unit cell are 
you using?  Could the protein be running into its own periodic image?

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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