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

[Graham J.A.]

Leila,

I have recently released a piece of software to assist in the creation
of CG models (particularly for use with MARTINI) from atomistic
simulations in the way Peter suggests, which you may find useful.

The documentation includes a brief tutorial, though it makes an
assumption of some familiarity with designing a good CG mapping.  I'd be
happy to discuss the mapping component in more detail with you and
perhaps add some more content to the tutorial.

Software: https://github.com/jag1g13/pycgtool
Tutorial: http://pycgtool.readthedocs.io/en/master/tutorial.html

End of somewhat-shameless self-promotion,

James


On Fri, 2017-02-03 at 14:56 +0100, Peter Kroon wrote:
> 
> Error verifying signature: parse
> error
> 
> 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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