GROMACS version: 2024.2
GROMACS modification: No
Hello, I’m currently analyzing a few molecules to cross Blood Brain Barrier (BBB). I tried creating BBB using MD Simulations. But, it’s not working anymore. Moreover, I’ve also tried with cgmartini.nl. But, that’s not quite user friendly and I’m confused about where and how to go about it. So, can anybody help me out with it…?
Dear @raannakasturi
The tutorial from Dr Lemkul is really great for many reasons, but luckily the process of building the membrane is relatively easier nowadays. Take a look at CHARMM-GUI, I guess this is arguably the most used tool to build bilayer boxed, and it should support Martini as well, now.
Thanks @obZehn , I’ve created the DOPC lipid bilayer using CHARMM-GUI and, I’m stuck about how to penetrate and pass the SDF molecule through the DOPC bilayer based on this paper https://pubs.acs.org/doi/10.1021/acs.jcim.9b00834. and, I’m trying to replicate this paper itself. Will it be possible for you to help me out? I’m relatively new to the Gromacs and a recent student of bioinformatics. So, I might need a detailed data or info regarding this
My two cents would be that it is better if you start from a simpler model rather than trying to build a bilayer out of scratch. So, by taking a look at the paper, I would just use CHARMM-GUI (as they did) to try to replicate one of their systems. Once you have it running and while it reaches equilibrium, you can parametrize a few molecules within CHARMM36m - for example with CGenFF - and learn about how to drive a molecule around with the pull module of GROMACS. A few good tutorials are here and here, specifically this one and this one for the steered MD passage which is usually the opener of umbrella sampling methods.
Thank you so much @obZehn for your help. I’ll try to do that.