Fwd: Coarse Graining Problem

From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Wed Feb 24 2010 - 05:59:51 CST

---------- Forwarded message ----------
From: Aditya Ranganathan <aditya.sia_at_gmail.com>
Date: Wed, Feb 24, 2010 at 4:07 PM
Subject: Coarse Graining Problem
To: majordomo_at_ks.uiuc.edu, vmd-l_at_ks.uiuc.edu

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Respected Sir,
I`ve been looking at various coarse graining methods available.
However, the CG Tools Residue Based Coarse Graining technique uses a 2
bead model of coarse graining (if I`m not wrong). However, from waht I
gather, 2 bead models are`nt accurate enough representations to study
more complex events like aggregation. I came across literature on the
internet where there have been mention of four or even six bead

Can you clarify whether a 4 bead model can be implemented and used in
VMD/NAMD or by any other tool?
Also, how would you rate the Shape Based Coarse graining methods
compared to the REsidue Based Method in terms of accuracy in case of a
protein aggregation/assembly study.

Srivastav Ranganathan
Junior Research Assistant,
Department of Biosciences and Bioengineering,
Indian Institute of Technology, Mumbai, India

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