Sorry,
I'm using Sander; I tried to use Pmemd but Pmemd does not support gbsa >0,
and then the error advices you to use Sander.
I searched for applications of implicit solvent but it's very difficult to
find people that discuss input script of a simulation..
I'm using implicit solvent in order to see how difference in salt
concentration could effect computationally the binding of protein with DNA,
that's why I'm using it.
Thanks for your help
2011/3/7 Carlos Simmerling <carlos.simmerling.gmail.com>
> you say you are using "Amber" but you don't say which program. For large
> systems, pmemd is much more efficient than sander. Also keep in mind that
> the tutorial options selected may not be appropriate for production
> systems.
> You should be looking for peer-reviewed and successful applications on
> similar problems and follow their methods. Tutorials are usually intended
> to
> help you learn the program and execution, and not to suggest best practices
> in terms of force field and model choices, and so on. GB models have well
> documented weaknesses (and benefits), and you need to think carefully about
> the potential impact on your project.
>
>
> On Mon, Mar 7, 2011 at 10:04 AM, Rubben Torella <rubben.torella.gmail.com
> >wrote:
>
> > Dear Amber community,
> > I'm trying to perform MD simulation in implicit solvent using Generalized
> > Born approach on a protein-DNA complex.
> > I followed the tutorial described here (
> >
> >
> http://www.uni-koeln.de/themen/chemie/software/amber7/tutorial/gb/gb_tutorial.html
> > )<
> >
> http://www.uni-koeln.de/themen/chemie/software/amber7/tutorial/gb/gb_tutorial.html
> > >in
> > order to set-up the calculation.
> > We are talking about 7637 atoms in the complex.
> > I launched the calculation on 64 processors (10 ns), but the calculation
> > seems to me very slow (1.3 ns/day)
> > Is there something wrong in this approach or is it normal to have this
> > calculation speed?
> > I attached you the input of the MD calculation, in order to know if there
> > are mistakes or there is some flags that slow down the calculation.
> > Thank you for your help
> > Rubben
> >
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> >
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Received on Mon Mar 07 2011 - 07:30:03 PST
