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-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] för Justin A. Lemkul [jalem...@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
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