It's certainly possible that the simulation becomes more efficient in later
steps, especially since the first steps have the setup and such. However,
it's trivial to calculate the ns/day that you achieve by looking at the
mdout file. Simply look at how long it took to complete your 10000 steps
and convert that into ns/day. (Simple dimensional analysis that we do in
our 1st chemistry class). In fact, that's how it's done for the mdinfo.
On Tue, Aug 17, 2010 at 11:55 AM, Mayank Daga <mdaga.vt.edu> wrote:
> What I am concerned is how would the ns/day be affected if and if not the
> simulations run to the entirety. The mdinfo file states ns/day obtained due
> to last 'x' steps, hence if the 'x' = 10000 and not 1000, is there a chance
> the average would be better for 10000 steps??
> ~mayank
>
> On Tue, Aug 17, 2010 at 11:31 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hello,
> >
> > I believe that pmemd does not update the mdinfo file as often as it
> updates
> > the mdout file due to performance implications. You can figure out the
> > source of this discrepancy by digging through the pmemd code, but this
> has
> > no effect on your results.
> >
> > Hope this helps,
> > Jason
> >
> > On Tue, Aug 17, 2010 at 11:10 AM, Mayank Daga <mdaga.vt.edu> wrote:
> >
> > > Hi,
> > >
> > > I am a newbie using AMBER on the GPUs.
> > > When I run my simulations, I see two output files, mdout and mdinfo. In
> > the
> > > mdinfo file, I see the timing details as to how many ns/day I get. The
> > > issue
> > > is some steps are always uncompleted according to this file while mdout
> > > lists that all the steps have been completed. Why is this discrepancy?
> > > For example, if I run a simulation for 10000 steps, mdinfo shows 9000
> > steps
> > > remaining while mdout list energy values for all 10000 steps.
> > >
> > > I am using the input files as downloaded from the AMBER website and to
> > run
> > > the simulation:
> > > ~/amber11/bin/pmemd.cuda -O -i mdin -o mdout -p prmtop -c inpcrd -r
> > restrt
> > > -x mdcrd -gpu 0
> > >
> > > Please explain this behaviour.
> > >
> > > Thanks,
> > > ~mayank
> > >
> > >
> > > --
> > > Mayank Daga | SyNeRGy Laboratory | Dept. of Computer Science
> > > Virginia Tech | http://synergy.cs.vt.edu | http://www.cs.vt.edu
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Mayank Daga | SyNeRGy Laboratory | Dept. of Computer Science
> Virginia Tech | http://synergy.cs.vt.edu | http://www.cs.vt.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 17 2010 - 09:30:03 PDT
