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

[Justin A. Lemkul]

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!

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

-Justin

> 
> Emma Eriksson PhD student in biophysical chemistry School of chemistry 
> National University of Ireland - Galway Galway, Ireland 
> ________________________________________ Från: gmx-users-bounces at gromacs.org
> [gmx-users-bounces at gromacs.org] för Justin A. Lemkul [jalemkul at vt.edu] 
> Skickat: den 29 april 2010 17:20 Till: Gromacs Users' List Ämne: Re:
> [gmx-users] Constrained simulations crash when bilayer moves  in      the z
> direction in the box
> 
> ERIKSSON, EMMA wrote:
> 
>> Pcoupl                   = Parrinello-Rahman pcoupltype               =
>> semiisotropic tau_p                    = 1.0 1.0e-14 compressibility
>> = 4.5e-5 4.5e-15
> 
> I would bet almost anything that this is the cause of your problem.  How did
> you come up with these bizarre values for tau_p and compressibility in the 
> z-dimension?  I recall another post where there was an issue of z-drift like 
> this one.  You're using a tau_p in the z-dimension of 1.0x10e-14 ps - I don't
>  even see how that's possible!  It is certainly far too strenuous for P-R 
> coupling, where you should probably be using tau_p on the order of 5-10 ps.
> The compressibility also doesn't make any sense to me.  4.5e-5 in all
> dimensions should suffice.
> 
> -Justin
> 
>> ref_p                    = 1.0 1.0
> 
> 
> 
> -- ========================================
> 
> 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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-- 
========================================

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

========================================