[gmx-users] Using g_membed with MD-CG

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Dec 28 10:27:07 CET 2012

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.



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

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