GROMACS modification: Yes/No
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I modelled a CG membrane (MARTINI) containing a transmembrane protein in phospholipid membrane and equilibrated it in presence of water and ions. Now, I want to study the interaction of a molecule (also a CG model) with this equilibrated system. I am a bit confused on thr next steps and would like your inputs on which of the following two approaches be used:
- Minimize the molecule in water and ions, extract pdb of the molecule from the minimized system and then combine with the equilibrated membrane?
- Combine the molecule with the equilibrated membrane and then minimize the combined system?
In case I would like to study a mixed AA-CG model (AA for molecule and CG for membrane), how should I proceed?
Any suggestions or directions to a tutorial will be helpful.
Thanks in advance.
“In case I would like to study a mixed AA-CG model (AA for molecule and CG for membrane), how should I proceed?”
To study such a mixed system, first of all you have to define properly interface between AA and CG: for example how the AA description interacts with the CG description and other way around and assure that those definitions fulfill the physics behind simulations. Better to use an already developed AA/CG model (if available).
In alternative you can run the whole system at CG level and then backmap to atomistic description to extract features at the atomistic level.
Thank you for your reply, Alessandra.
Any thoughts about the Minimisation steps?
Concerning the energy minimization step, it depends on the origin of the structure. If it is a model, it is good run energy minimization before embedding it in the membrane.
After embedding the molecule in the membrane, energy minimize the system.