[gmx-users] Using g_membed with MD-CG

[Kieu Thu Nguyen]

Thank Tsjerk !

What is the different way that can convert the lipids ?

Regards,

KT


On Fri, Dec 28, 2012 at 4:27 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi KT,
>
> Either way should be fine. g_membed is not linked to a specific force
> field, so you can use it for coarse grained models too. You can also first
> set up an AA model and convert to CG afterwards. However, martinize.py only
> works for the protein, so you have to convert the lipids in a different
> way.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Dec 27, 2012 at 2:00 AM, Kieu Thu Nguyen <kieuthu2212 at gmail.com
> >wrote:
>
> > Dear All,
> >
> > When using g_membed tool to embed protein into membrane, can i use
> Martini
> > forcefield to generate the topology file ?
> >
> > Or can i use the all-atom forcefield to generate the .top file, and after
> > protein have inserted, AA representation have converted into CG
> > representation by using martinize.py ?
> >
> > Thank for any advice !
> > Best regards,
> > KT
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Biocomputing Group
> Department of Biological Sciences
> 2500 University Drive NW
> Calgary, AB T2N 1N4
> Canada
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