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

[Peter Kroon]

Hi,


you'd best redirect this question to the Martini forum (cgmartini.nl),
since this is more of a forcefield question than a Gromacs question.

To answer your question: if at all possible, stick to the 36 Martini
bead types available, and look at the tutorials on the Martini webpage.
There's also one on parametrizing a new molecule.


Peter


On 03-02-17 09:47, leila karami wrote:
> Dear gromacs users,
>
> I want to do MD simulation of peptide amphiphile using CG method.
>
> My molecule is shown in the following link:
>
> https://ln.sync.com/dl/db2c92bf0#i8jm6yin-5uz4tn32-nq37ewxa-3vrkmt4b
>
> Can I use the default beads definition for my molecule (containing
> hydrocarbon chain and amino acids)?
>
> What itp files should I include in topology files?
>
> martini_v2.2.itp
> martini_v2.2_aminoacids.itp
> martini_v2.0_lipids.itp
> martini_v2.0_ions.itp
>
> I am a beginner in CG method. Any help will highly be appreciated.
>
> Best,