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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
