VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 26 2013 - 10:01:37 CDT

Hi,
  I believe that if you want to know details of this sort, the two
best options are either to contact the authors of the research papers
on the method, or two simply read the source code for the CGTools
plugin that they developed. The second may be a faster way to answer
your questions in detail since all of these people have moved at least
once or twice since the CGTools papers were written. You can read the
code by looking in your $(VMDDIR)/plugins/noarch/tcl/cgtools1.0/
where $(VMDDIR) is replaced by the location of your VMD installation
directory on your machine (usually /usr/local/lib/vmd).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 26, 2013 at 08:04:21AM +0800, WuChaofu wrote:
> 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/~kvandiv! o/ Un iversity of Illinois
> > Phone: (217) 244-5711 405 N. Mathews Ave
> > Fax : (217) 244-6078 Urbana, IL 61801, USA 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/