[gmx-users] semiisotropic pressure coupling.

[Miro Astore]

Incredible thank you.

On Wed., 15 Apr. 2020, 8:46 pm Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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