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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--
========================================
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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