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

ERIKSSON, EMMA E.ERIKSSON1 at nuigalway.ie
Thu Apr 29 18:25:55 CEST 2010

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...

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


> 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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