[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 18:20:40 CEST 2010


> 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.


> ref_p                    = 1.0 1.0


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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