[gmx-users] semiisotropic pressure coupling.

[Justin Lemkul]

On 4/14/20 10:12 PM, Miro Astore wrote:
> 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

This was due to a CHARMM-specific bug in which CMAP forces were not 
correctly calculated when two atoms were in different periodic images: 
http://manual.gromacs.org/current/release-notes/2019/2019.4.html#fix-incorrect-pressure-when-atoms-in-cmap-cross-a-box-boundary

It was fixed in version 2019.4.

Update your GROMACS version and you don't have to try playing any tricks 
like zero compressibility.

-Justin

> 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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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