VMD-L Mailing List

From: masoumeh ozmaeian (ozmaian83_at_gmail.com)
Date: Sun Oct 31 2010 - 13:37:18 CDT

Sorry fot that.
It's obvious I have force fields parameters. I meant it's not in a special
data format for VMD.

and this is my previous email:

"First thanks indeed for your considerations.
In my previous simulations I worked with proteins and DNAs. This is my first
time for polymers. I don't have the compatible file for CHARMM( I mean it's
not in a special data format for VMD). This polymer consists of 10 monomers.
In the other word I have a 680 atomic chain. I have about 200 water molecule
around it."

Bests,

On Sun, Oct 31, 2010 at 10:12 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sun, Oct 31, 2010 at 3:08 AM, masoumeh ozmaeian <ozmaian83_at_gmail.com>
> wrote:
> >
> > I didn't receive any more answers. Does it mean I can't do that without
>
> you didn't receive any answers, because you didn't reply to the mailing
> list.
>
> > charmm compatible topology and parameter files?
>
> please use your common sense! how would it be possible to do
> an MD simulation without parameters?
>
> a.
>
> > On Sun, Oct 17, 2010 at 10:06 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Sun, Oct 17, 2010 at 3:26 AM, masoumeh ozmaeian <ozmaian83_at_gmail.com
> >
> >> wrote:
> >> > Dear all,
> >> > Hi,
> >> >
> >> > I'm trying to make a psf file of a pdb polymer chain( Nafion) and the
> >> > force
> >> > field is Charmm.
> >>
> >> > Is it possible and how?
> >>
> >> the answer to the first part of your question is "yes".
> >> the answer to the second part of your question is
> >> "it depends". in principle, there is nothing difficult
> >> about generating a psf file, particularly for a rather
> >> simple polymer. in practice, there are a lot of devils
> >> hidden in the details. before going any further, a
> >> few questions back:
> >>
> >> what experience do you have with MD and building topologies?
> >> do you have chamm compatible topology and parameter files?
> >> is the pdb file for the polymer or just a monomer?
> >> if the former, does it include water?
> >>
> >> cheers,
> >> axel.
> >>
> >> >
> >> > Bests,
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> >> http://sites.google.com/site/akohlmey/
> >>
> >> Institute for Computational Molecular Science
> >> Temple University, Philadelphia PA, USA.
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>