VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 31 2010 - 13:54:12 CDT

On Sun, Oct 31, 2010 at 2:37 PM, masoumeh ozmaeian <ozmaian83_at_gmail.com> wrote:
> Sorry fot that.
> It's obvious I have force fields parameters. I meant it's not in a special
> data format for VMD.

VMD doesn't do any simulation. you need the parameters in
a format suitable for the MD code that you want to use. several
codes can read multiple topology file formats or have tools
to convert between them.

and there are multiple ways to go about creating the necessary
topology and coordinate information within VMD, too.

VMD originates in bio simulations and thus the majority of
its tools are optimized for such simulations. however, that
doesn't mean you cannot use it for other systems, but you
have to be more creative and cannot just blindly use the
same methods and strategies. if you _do_ want to use the
same scheme (and psfgen), then you indeed have to produce
the proper residue templates in the proper format. i have
never done this, but there are tutorials for that on the TCBG
home page somewhere. for simple polymers, using the
topotools plugin can be a good alternative, although you will
have to do a few more manual steps. but then again, topotools
is not confined by the assumptions of psfgen.
i (and others) have been using it to build topologies for LAMMPS,
but it works just as well for generating the information that can
be saved to a .psf file (actually, a .psf file contains less information
than a LAMMPS topology aka data file).

for the rest, you need to use common sense and teach yourself
sufficient skills in scripting.

axel.

> 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.
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.