[gmx-users] semiisotropic pressure coupling.

[Miro Astore]

Hello all,

I am working with a rather large membrane bound protein. I was getting
an issue awhile ago where if the protein moved to the edge of the box
the box would elongate in the z direction. I fixed this in the short
term by setting my xy compressibility to 0 in my production mdp file
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0

compressibility         = 0  4.5e-5
ref_p                   = 1.0     1.0
compressibility         = 0  4.5e-5
ref_p                   = 1.0     1.0

I have a few questions, why was it blowing up in the first place? I
would guess its to do with how the pressure is being calculated when
this large 'vacuum' is being created in the solvent when the protein
wraps around since my tc_grps is Protein non-Protein. The fact the
problem only occurs when the protein wraps seems to indicate this sort
of artifact, I can get into the hundreds of nano seconds before the
protein drifts if I'm lucky, this is all after a well equilibrated
system.

I could fix the protein in the center of the box but I fear that might
produce artifacts and I suspect there is a better way.

I want to start studying how this protein interacts with the lipids
and fixing the xy box size is not conducive to this so I'm wondering
how  I can let the lipids fluctuate while still maintaining sensible
system behavior.

Thank you for your time,

Best, Miro

mdp file can be found at
https://docs.google.com/document/d/16vsS4OOco9U3bUkarzSduN2OXohnBVVLedwLJanUi4w/edit?usp=sharing
--
Miro A. Astore   (he/him)
PhD Candidate | Computational Biophysics
Office 434 A28 School of Physics
University of Sydney