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

Peter Kroon p.c.kroon at rug.nl
Fri Feb 3 14:56:20 CET 2017

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.


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