Requesting for assistance

saysayani11 / Nanoparticle-Bilayer-Dynamics

A molecular dynamics approach to study the permeation of nanoparticles through lipid bilayer

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Requesting for assistance #1

Open RaannaKasturi opened 2 months ago

RaannaKasturi commented 2 months ago

GROMACS version: 2024.2 GROMACS modification: No

Hello, I'm currently analyzing a few molecules to cross 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (DOPC) bilayer. I tried creating DOPC bilayer 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 youhelp me out with it..?

saysayani11 commented 2 months ago

Sure. Could you possibly share your starter files, and point me out the issue your are facing?

RaannaKasturi commented 2 months ago

Actually, 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?

RaannaKasturi commented 1 month ago

Any update?