VMD-L Mailing List

From: WuChaofu (xiaowu759_at_hotmail.com)
Date: Mon Mar 25 2013 - 19:04:21 CDT

Dear Vandivort,
Thank you very much for your reply. In fact, I have read the web page and the reference as you pointed out. But I am stil a bit puzzling about the theory since it is not described in detail. I am wondering whether no rotation is carried out, namely only translation is performed on the previous atoms before mapping when all atoms mapped on the CG are backmappingly placed on the center-of-mass of the CG bead. Could you give me some hints, please?
Chaofu Wu
> Date: Mon, 25 Mar 2013 15:37:55 -0500
> From: kvandivo_at_ks.uiuc.edu
> To: xiaowu759_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Theory of backmapping of CGTools
>
> On 03/25/2013 07:06 AM, WuChaofu wrote:
> > Dear vmders,
> > I try to use the backmapping of CGTools, namely, to generate an atomistic model
> > from an CG model. However, I can not find the underlying theory to do so for
> > CGTools. Could you give me some explanations, please?
> > Chaofu Wu
> > xiaowu759_at_hotmail.com <mailto:xiaowu759_at_hotmail.com>
>
>
> Chaofu,
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/ gives some additional
> detail on doing reverse coarse graining, including references to journal
> articles discussing this topic. Specifically, refer to the section entitled:
> Reverse Previously RBCG Model Back To All-Atom. Briefly, when you create a
> coarse grain model using Residue Based Coarse Graining, a data file is created
> that stores required mapping information that can then be used during the
> conversion from CG to all atom.
>
> --
>
> Kirby Vandivort Theoretical and
> Senior Research Programmer Computational Biophysics
> Email: kvandivo_at_ks.uiuc.edu 3061 Beckman Institute
> http://www.ks.uiuc.edu/~kvandivo/ University of Illinois
> Phone: (217) 244-5711 405 N. Mathews Ave
> Fax : (217) 244-6078 Urbana, IL 61801, USA