Dear all,
I am new to GROMACS and I am trying to understand how to properly build and run a simulation of a lipid bilayer. In particular I am trying to build a lipid bilayer made of three kind of lipids: a free fatty acid (lignoceric), a cholesterol and a ceramide (cer2).
I downloaded the structure files and the force field from ATb (GROMOS 54 a7). Then, following the workflow of Justin Lemkul's second tutorial, I built my lipid bilayer system and run the first equilibrium stages. The problem is the following: once I start my unconstrained NPT production, ceramides and fatty acids stay in their position while many cholesterol molecules leave the lipid bilayer and move "inside" the bilayer, so in between the two leaflets. I know that it is possible that some cholesterol molecules can do this thing, but in my system this happens to too many of them (~30/40%). Honestly it seems really unreasonable and that's why I am here: did any of you have the same problem? Is it related to some kind of bad initial structure?
Hi Nicola,
Perhaps it is due to an error in the construction and minimization of your initial topology, you could choose to generate your initial structure with CHARM-GUI and follow the tutorial you mention.
http://www.charmm-gui.org/?doc=input/membrane.bilayer Good luck
If you are struggling with a specific lipid type, it might be that your force field doesn't have all of the parameters it needs to have. I'm not familiar with the ff your downloaded and if you needed to make any modifications to it.
Since you are starting out, I agree with Martiniano Bello that building with the CHARMM-GUI for building lipid systems is the easiest way to proceed. You may also want to perform your simulation in CHARMM. Some of the developers have been specifically interested in modeling lipid bilayers with varying lipid types and so, in my opinion, it is pretty well set up to do that. You might refer to some of the works of Jeffrey Klauda's lab at UMD to find a protocol for their lipid simulations, and online tutorials.
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