[gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> ERIKSSON, EMMA wrote:
>> I was using those "strange" values of tau_p and compressibility to 
>> keep the z
>> box length fixed in order to avoid problems associated with scaling the
>> positions of the molecules in the box when we constrain the distance 
>> between
>> DPPC and the small molecule. I was told to use those values but maybe 
>> it's
>> not correct...
>>
> 
> I would certainly try to eliminate it as a possibility.  I just don't 
> know how the pressure coupling algorithm could possibly handle a tau_t 
> that is several 10e-11 times smaller than the timestep!
> 

*Edit* That should read "tau_p."

> A well-equilibrated system should not fluctuate substantially over the 
> course of a simulation, anyway.  But if you need to fix the box, you 
> *may* be able to set the relevant values of tau_t and compressibility to 

*Edit* This should also read "tau_p."

> zero (as in the case of tau_t for temperature coupling), but I have 
> never tried it.
> 

This one's right :)  Apologies for any confusion, my brain was going faster than 
my fingers on this reply!

-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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