How to simulate a preprepared membrane model?

29 June 2024 1 6K Report

I have a membrane model files from a published work. I want to use that model for my research. Can anyone help me with how do I proceed with it. I have the PDB, PSF and STR files of the membrane.

I am using gromacs 2021.4 version.

Specifically, I would appreciate your guidance on the following points:

Creating the topol.top file: What elements should be included in it and where should they be placed?

Placement of .str files: Should these files be placed in the forcefield folder (I am using the CHARMM36 forcefield downloaded from the CHARMM website) or in my working directory, and how should they be defined in the topol.top file?

Annemarie Honegger

Start here:

Running membrane simulations in GROMACS:

https://manual.gromacs.org/current/how-to/special.html

Introduction to Membrane-Protein Simulation: https://tutorials.gromacs.org/membrane-protein.html

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