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

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 29 18:39:51 CEST 2010

Justin A. Lemkul 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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