VMD-L Mailing List

From: Dudo (dudomail_at_gmail.com)
Date: Wed Feb 08 2012 - 18:47:01 CST

http://www.youtube.com/watch?v=HZbR6w0Y7xU

On Thu, Feb 9, 2012 at 12:35 AM, kirtana S <skirtana4_at_gmail.com> 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
>
> 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.
>
> Thanks for response
> Kirtana
> 

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