Re: [AMBER] Simulation of an asymmetric membrane model

From: Matias Machado <>
Date: Thu, 13 Feb 2020 16:37:33 -0300 (UYT)

Dear Eduardo,

Despite using a staked membrane system is a standard setup for setting asymmetric ionic concentrations, it may be very computational expensive... (you have duplicate or triplicate the system!!!)

In that sense, there are also other possibilities, see for example:

+ Modeling Membranes under a Transmembrane Potential []

+ Salt induced asymmetry in membrane simulations by partial restriction of ionic motion []

+ Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations []

Some of those approaches may not be used in AMBER due to technical reasons. In particular the second strategy is very easy to use, but it requires of restraining the movement (position) of particles on one coordinate (z axis). That can't be done in AMBER (it's all "xyz" or none), but it can be done in OpenMM or GROMACS. I thick that would be a very nice feature to have in AMBER, which could also help the equilibration of protein-membrane systems by allowing the free diffusion of lipids in the z plane while keeping the desired thickness of the bilayer...

Any way... there's still another alternative, which can be done in AMBER but we haven't tested it yet... It implies using a multi-scale setup with our coarse-grained water model (called WT4) of the SIRAH force field. The related paper is the following:

Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk []

The idea is to set the system as sandwich like this:

 | -----------
 | WT4 (no ions)
 | -----------
 | ooooooooooo
 | ||||||||||| Membrane (+ protein)
 | |||||||||||
 | ooooooooooo
 | -----------
 | WT4 (no ions) # Notice: Due to PBC, there is no need to actually set this slab
 | -----------

Because WT4 and TIP3P experiences a limited mix and atomistic ions ALWAYS remain within the atomistic solvent phase you can generate an asymmetric ion distribution at NPT without restrains! yeah that sounds cool... but wait! even better, it shouldn't have a significant computational cost as WT4 is a CG model ;-)

You can find native ports of SIRAH for AMBER at []. The multiscale solvent is already implemented in the released version of the package but we have to post some tutorials about that...



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "ABEL Stephane" <>
Para: "AMBER Mailing List" <>
Enviados: Jueves, 13 de Febrero 2020 6:37:43
Asunto: Re: [AMBER] Simulation of an asymmetric membrane model


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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