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