VMD-L Mailing List

From: kirtana S (skirtana4_at_gmail.com)
Date: Wed Feb 08 2012 - 17:35:26 CST

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