On 03-02-17 13:01, leila karami wrote: > 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. Sorry about that, I must've missed your post completely. > >> 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? Run a short atomistic simulation in your ff of choice, and use the distribution of bond lengths found there to determine the parameters you need. You may need several iterations.
Peter
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