Thank you Dan, I'll try to compare it and then I can evaluate.
Do you know which is a reasonable cutoff for a complex?
Is there some empirical analysis (distance?) to find the best cutoff for
your system?
2011/3/7 Daniel Roe <daniel.r.roe.gmail.com>
> My apologies, I was looking at the wrong mdin - the cutoff is 300 only
> for the minimization, not the production run.
>
> However, you should still run the included benchmarks and compare.
>
> -Dan
>
> On Mon, Mar 7, 2011 at 10:40 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> > Hi,
> >
> > You are running GB with an extremely large cutoff (300.0 Ang) so I
> > think that 1.3 ns/day is not unreasonable for ~7600 atoms.
> >
> > Also note that your specific system setup (CPU, interconnect speed,
> > compilers used etc) will impact your timing. You can run the
> > benchmarks included with Amber and compare to existing benchmarks
> > (http://ambermd.org/#benchmarks) to get an idea for how your system
> > measures up.
> >
> > -Dan
> >
> > 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 - 08:30:04 PST
