normal CG simulations of a membrane protein with an applied electric field?

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5 months 3 weeks ago #7791 by mprevost

I am trying to simulate a CG system containing a membrane protein subjected to an electric field.
I constructed the system with Charmm-gui and ran the first minimisation and equilibrations with the Charm-gui grimaces input file without problems.
A following equilibration with an imposed electric field of Ez=10 V/nm crashes. Reducing the electric field to 0.5 solves the problem. However the molecular system shrinks along the Z direction (direction perpendicular to the membrane) to an almost 2D system!

Could you tell me what's wrong? Can one simulate a CG system with an applied electric field?

Thanks on advance for your help.

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5 months 1 week ago #7803 by bart
Could it be that you box is set to semiisotropic and that the imposed electric field introduces pressure in z? Then the box would adept to that, squeezing it smaller and smaller. A solution could be to to do nvt or to set the box to isotropic, or maybe the best, to meassure the imposed pressure and set the z pressure to the new imposed level for the barostat and keep it at npt semiisotropic.

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