VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Feb 28 2012 - 16:53:50 CST

Kirtana,

On 02/08/2012 05:35 PM, kirtana S wrote:
> I am using the coarse grain plugin in VMD. The method used is residue based
> coarse graining method.I have some questions
> on the CG database file format.
> What does the numbers specified on the third column of the file represent.Again
> why we have H2O and OH2.
> Is this for 3 monomer units of water.
> I am using this for a polymer chain polystyrene. Here each monomer represents a
> single residue.So Should I do this as below
> CGBEGIN
> RES1 (C6H6)CH3 0
> RES1 C1 0
> RES1 C2 0
> RES1 C3 0
> RES1 C4
> RES1 C5
> RES1 C6
> RES1 C7
> RES1 C8
> RES1 H1
> RES1 H2
> RES1 H3
> RES1 H4
> RES1 H5
> RES1 H6
> RES1 H7
> RES1 H9
> RES1 H10
> RES2 (C6H6)CH2
> RES2 C1
> RES2 C1

The CG database file format is described in the help for the CG Tools plugin at

http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/

If you scroll to the bottom of the page, you will see an example file with an
explanation of the format.

> And so on till CGEND for all the monomers in the chain or should I change . Also
> when I do this I have loaded .mol2 file.
> This prompts me to have .psf file. Where should I load this .psf file.

The PSF file should be loaded into the molecule you are wanting to coarse grain. 

-- 
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) 244-1928                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA