[AMBER] Simulation protocol for Ionic Liquid (IL) - Bilayer system

From: Delwakkada Liyanage, Senal Dinuka via AMBER <amber.ambermd.org>
Date: Sun, 4 Jun 2023 19:01:03 +0000

Dear AMBER users,

I hope this email finds you well. I am reaching out to seek your guidance and best practices as experienced AMBER users for simulating a POPC-IL system. I am relatively new to simulating lipid bilayers, and this is my first attempt at building a 100% IL solvent system from scratch.

The system consists of a POPC lipid bilayer generated using CHARMM-GUI, comprising 144 lipid molecules. Additionally, I have included 1300 choline and lipoate ions positioned 70 A above and below the lipid bilayer (Z=190). The dimensions of the modeled system are X=Y=110 A.

I have come across some guidelines in the literature, which I plan to use as a starting point for designing my simulation protocols.
To give you an overview of my current protocol:


a. Minimized the IL with restraints (at least 1000) on the lipid bilayer.
b. Minimized the lipid bilayer with restraints (at least 300) on the IL.
c. Minimized the entire system without any restraints.


conduct a 10 ns NVT MD run at 310 K, with the lipid molecules fixed to ensure proper hydration of the system. The protocol was adapted from https://doi.org/10.1021/acs.jpcb.6b08059.


semi isotropic NPT simulation (simulated annealing required or not?)
vdw and electrostatic cutoff of about 1.2 nm ?

Best regards,
Senal Liyanage


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Received on Sun Jun 04 2023 - 12:30:02 PDT
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