Re: [AMBER] Simulation of an asymmetric membrane model

From: ABEL Stephane <>
Date: Thu, 13 Feb 2020 09:37:43 +0000


You could construct three stacked membranes to have a constant ionic concentration in the both sides of the central membrane


De : Eduardo R. Almeida []
Envoyé : mercredi 12 février 2020 20:38
À :
Objet : [AMBER] Simulation of an asymmetric membrane model

Dear Amber users and developers,

I am preparing a membrane model that includes a specific lipid composition and concentrations of different ions (Na+, K+, Ca2+, Mg2+, Cl-). In order to build this asymmetric system, I used both CHARMM-GUI and packmol utilities. However, in order to properly simulate this system, the ionic concentrations must be constants in the inner leaflet and outer leaflet throughout the simulation, since there is a notable ionic gradient between the intracellular and extracellular regions in mammalian cells. I tried to use the conventional periodic boundary conditions (PBC) in my simulations (ntb = 2), but I noticed that the ionic concentration in each leaflet did not remain constant during the simulation. On the other words, it seems that the ions migrated between the cell images mixing the ionic concentrations. In this sense, I would like to know if there is a way to keep the number of ions in each leaflet constant during all simulation avoiding the migration of ions from one layer to !

Best regards,


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