normal Simulation blows up when the protein crosses periodic boundary

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1 year 6 months ago #7412 by h_and
Hello,

I simulate modelled proteins in bilayer using elnedyn 2.2p. I energy minimize my system and do backbone-restrained NVT and NPT equilibrations with gradually increasing time steps. When I start MD production there is no problem with my system but blows up after several nanoseconds (usually around 200-400ns).
I realized that the LINCS warnings preceeding the explosion happen when my protein starts to cross the periodic boundary. I also observed that at least one of the affected beads are S-beads (histidine or triptophan).

I tried to change several options to circumvent this problem: longer energy minimization, equilibration, decreasing time steps. When I martinize my protein I receive the warning that elnedyn topologies are stable only if the mass of S-beads are set to 72. I did that but did not help. The only way I could avoid blowing up is using Berendsen pressure coupling instead of Parrinello-Rahman. I experienced this on several kind of membrane-embed proteins, no matter how it is generated (Charmm-GUI or martinize+insane).

What could be wrong with my system? Is there anything that I am missing?



MDP options are below. I can share my itp and tpr files if necessary.
I always run my multi-threaded simulations with the parameter -rdd 1.4.
Gromacs version: 5.1.4
martinize.py version: 2.6
particle definition: martini_v2.2refP.itp

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1 year 6 months ago #7415 by peterkroon
Heyhey,

Nothing looks really wrong at first glance, so that's good. Since you're using 2.2P you should probably consider using PME (or maybe RF) for the electrostatics and polarizable water.
Being close to the periodic boundary should not make any difference (otherwise it's a Gromacs bug). Are you sure the pressure is converged after your equilibration? You could try increasing tau-p to, e.g. 24. And personally I'd set -rdd 1.6, but I don't think that'll matter here.

Peter

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1 year 6 months ago #7445 by h_and
Setting tau-p to 24 helped, thank you very much.

To answer your question: Yes, the pressure converged, the crash actually happened long-long time after equilibration (even microseconds sometimes). The only common pattern in my crashed simulations was the protein crossing the periodic boundary. It seems that higher tau-p solves this problem.

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