[gmx-users] Own Coarse Grained ff
jalemkul at vt.edu
Tue Nov 20 17:40:01 CET 2012
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
> 2. How can I get bonded parametrs between my beads?
How do other CG force fields do it?
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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