Re: * CGtool force field *

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Oct 22 2011 - 12:47:47 CDT

On Sat, Oct 22, 2011 at 1:00 PM, HAMID - <h2a1385_at_gmail.com> wrote:
> Dear all,
>
> I am looking forward to every one answer my previous post about RBCG water.

dear hamid,

if you don't get an answer, then usually for a reason.

perhaps nobody thought that your question was
worth answering, perhaps people thought the answer
is too obvious, perhaps people didn't understand
the question, perhaps nobody knows an answer.
 the remedy for each of these is that *you* have
to think more about your problem, work harder
and come up with a better/simpler question instead
of complaining about not getting any. complaining
only makes it _less_ likely to get a qualified answer.

> I check the RBCG water bead top and parameter file which implemented
> in CGtool folder of VMD.
> Again I see the water beads in RBCG have zero charge thus, such water

pop quiz: what does a water bead in this model
represent and what is the total charge of that?

> model does not able to reproduce electrostatic interactions and I
> think it is a disaster for my simulations.

well, like the saying goes: if the cap don't fit, don't wear it.

> Does any one introduce me a method to compensate the absence of water
> charge effects in my RBCG simulations (simulation of a huge protein
> complex - protein interactions)?

this is a question that is best answered by studying
the literature. it looks to me that you are very confused
about what a coarse grain model can do and what not.
it is pointless to study something that cannot be properly
represented with a model you chose. you wouldn't want
to use a classical force field to study bond breaking,
or would you?

> I would really appreciate any guide.

my advice: get busy learning the method and its background
before actually starting something that may be a waste of time.

axel.

>
> Best.
>
> ----
> H. Hadi
> PhD student of Biophysics,
> UT, Iran
>
>

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

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