[gmx-users] How to build a coarse grained model and do the simulation with Gromacs

[Justin A. Lemkul]

٩ wrote:
> Dear Gromacs users
> I'm sorry the topic is not so clear. I have run a atomic model for a few 
> times, and the system that I want to simulate is too large to run. Now I 
> have to build a coarse grained model of lipid bilayer. Is there anyone 
> who has the experience?
> I've heard that one user just success in buiding his own force field 
> file, I think that's what I should do when I buiding the model.
> Here is my plan:
> 1. write a gro/pdb file of the model (can VMD do this?)

VMD will create an all-atom force structure.

> 2. write force field file and .itp/.rtp file
>  

You could do that yourself, but it would be quite a task for a new user.

> What should I do next? So confused.
> Is there any software could help me to do this more convenient? I've 
> just learned Vi.
> Any suggestion is welcome.

Probably the easiest thing for you to do is check out the MARTINI force field:

http://md.chem.rug.nl/~marrink/coarsegrain.html

There are structures and topologies available for a variety of pre-equilibrated 
bilayers.

-Justin

> Thank you for your help!
> 
> Frank Lai
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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