[gmx-users] Own Coarse Grained ff

[Justin Lemkul]

On 11/20/12 9:02 AM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I want to simulate protein based on my own LJ parameters between
> different types of residues. I will be given sets of parametrs for
> given sizes of beads to then apply them and valide by atomistic
> simulations. My question:
> 1. What is the best way to build different sizes of beads for given
> pdb file? Any softwarer?

I would think the apparent "size" of a particle is governed by its LJ terms, 
thus defining the location of the well depth for inter-particle interactions. 
Van der Waals radii and such are not used in any component of the input files in 
Gromacs.

> 2. How can I get bonded parametrs between my beads?
>

How do other CG force fields do it?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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