VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Thu Jun 13 2013 - 09:24:54 CDT

On 01/-10/-28163 01:59 PM, WuChaofu wrote:
> Dear VMDers,
> I try to use the cgtools to reverse map one coarse-grained model to its all-atomistic counterpart. To understand the principle underlying this plugin, I look through the script cgtools.tcl. I find I can not work out what the "revbonds" means. Could you explain to me, please? Thanks a lot.
> Yours sincerely,
> Chaofu Wu
>

Chaofu,

I've been out of the country for a while. Sorry for the slow response. In case
you haven't already figured it out,

The 'revbonds' parameter to the apply_reversal procedure lets you decide whether
or not you want CG tools to try and keep the atoms with inter-bead bonds as
close as possible to their original position by rotating the beads. If you want
to see the algorithm for exactly how this is determined, search for 'compos' in
the cgtools.tcl file. 

-- 
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