AMBER Archive (2008)

Subject: Re: AMBER: diblock copolymer

From: Z Insepov (insepov_at_gmail.com)
Date: Tue Jan 22 2008 - 23:23:39 CST

Thanks alot. I know about the CG-MD. I thought I need to run AMBER before
the CGMD as the force constants in CGMD should be obtained from an all-atom
MD.

Zee

On Jan 22, 2008 7:01 PM, Jed W Pitera <pitera_at_us.ibm.com> wrote:

> To my knowledge, nobody has tried to use AMBER to simulate diblock
> copolymers. The AMBER force fields are relatively detailed all-atom
> forcefields that have primarily been parameterized for biomolecules
> (proteins, nucleic acids, small molecule ligands) in water solution.
> There
> are no pre-existing parameter sets for typical monomers (polystyrene,
> polyethyleneoxide, pMMA, polyisoprene, etc.) seen in diblock copolymers
> although you could certainly generate them using ANTECHAMBER if you'd
> like.
>
> If you are interested in phase behavior and morphology, it will be
> difficult to access the necessary length (100 nm+) and time/energy scales
> using any all-atom forcefield, especially with molecular dynamics
> sampling.
> Most people working in this area use some sort of coarse-grained
> representation (e.g. bead-spring chain with LJ/WCA interactions) and often
> use Monte Carlo rather than MD. The only rationale I can see for
> simulating one of these systems in an atomistic model is if you're
> interested in the detailed interaction of some small molecule (solvent, a
> drug molecule, etc.) with the polymer.
>
> I would suggest that you take a look at recent references from places like
> the de Pablo and Glotzer groups if you want some examples; there is also a
> good review entitled "Monte Carlo simulation of block copolymers" by
> Binder
> and Mueller (Curr. Opin. Coll. & Interf. Sci 2000) that will help.
>
> --Jed
>
> PS: I am happy to answer further questions in this area, but they
> probably
> don't belong on the AMBER reflector.
>
>
>
>
> "Z Insepov"
> <insepov_at_gmail.co
> m> To
> Sent by: amber_at_scripps.edu
> owner-amber_at_scrip cc
> ps.edu
> Subject
> AMBER: diblock copolymer
> 01/17/2008 07:27
> AM
>
>
> Please respond to
> amber_at_scripps.edu
>
>
>
>
>
>
> Is there any simulation done on diblock copolymers by using AMBER force
> field?
>
> Z. Insepov
>
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