[gmx-users] MD simulation of peptide amphiphile using CG method

[leila karami]

Dear Peter,

Thanks for your answer.

> you'd best redirect this question to the Martini forum (cgmartini.nl),

> since this is more of a forcefield question than a Gromacs question.

You are right. At first, I asked my question in  Martini forum, but no
one didn't answer me.

> look at the tutorials on the Martini webpage.

There are tutorials for protein and lipid molecules separately, while my
molecule contains some amino acids bonded covalently to hydrocarbon chain.

> There's also one on parametrizing a new molecule.

In this tutorial, DPGS lipid was selected for the template. In this case,
only beads were displaced, while in my molecule, there is a new covalent
bond. My main question is how to treat with that?