VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Feb 02 2018 - 09:21:52 CST

Hi Soroush, VMD supports model building with the CHARMM force field
natively. If you're using CHARMM (note: that is entirely *your* choice:
there are many others) you only need to find force field files with support
for PEG chains, or build them yourself. Searching the literature or the
CHARMM forum may be a good start.

Once you have force field files, VMD has a couple of tools that can help
build and manipulate the system topology (PSF file):
http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/

As for generating an initial set of coordinates (PDB file), a couple of
independent tools may be of help:
http://www.moltemplate.org/
http://montecarlo.sourceforge.net/emc/Welcome.html

As for the number of polymer chains, you have to decide.

Giacomo

On Fri, Feb 2, 2018 at 8:21 AM, soroush ziaei <soroush.ziaei7337_at_gmail.com>
wrote:

> hi there,
> i'm a researcher & i want to simulate some polymer such as PEG on CNT;
> how can i adding this polymer to the surface of CNT, wrapping or adding
> to the edge of CNT ?
> if wrapping around the CNT is the best item please tell me how to wrapping
> this polymer;
> by the way how many monomers needed? and how to repeating this monomer to
> build the polymer?
> if there is a site that can generate polymers in pdb,... format, tell me.
> thanks a million.
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin