it's possible he means normal REMD, but run serially. no reason they need to
run simultaneously- I think Pande may have done something similar. it's just
going to take a very long time in wallclock. also the code is not set up for
this at present.
On Tue, Aug 23, 2011 at 4:04 PM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> Dear Dmitry
>
> What you suggest is possible and people have called that serial exchange
> I think, or even serial tempering, depending on he literature. What you
> are missing here (I think) is that you would have ONE replica traversing
> temperature space. Of course, given infinite time it works, but at each
> exchange point you get to move to the next higher or lower temperature.
> What replica exchange (as usually understood) has are N replicas doing
> this at the same time. So, you can exchange between T1 and T2 and AT THE
> SAME TIME exchange between T10 and T11 for instance. That added
> dimension is crucial for things to work well.
>
> Adrian
>
>
> On 8/23/11 3:59 PM, Dmitry Mukha wrote:
> > )) ok, I definitely have more CPUs than just one, but also I am also sure
> > that their number is not enough. the system is quite large, so I want to
> > have a lot of replicas covering high temperature values and the
> performance
> > good enough to see the effect of a traveling across temperature. Some
> kind
> > of exhaustive phase space search.
> >
> > Maybe, it would be rather difficult [to rewrite the code], but memory
> data
> > can be saved, thus decreasing the time for restart (without dumping to
> > disk). I guess there is a lot of tricks here possible.
> >
> > 2011/8/23 Carlos Simmerling<carlos.simmerling.gmail.com>
> >
> >> it usually takes programs some time before they become efficient. the
> >> spatial decompositino and load balancing are not ideal at the start.
> >> additionally, much work needs to be done to start running MD, such as
> >> reading and writing to disk, setting up the arrays, and so on.
> >> stopping the program each ps or less would be quite slow. are you in a
> >> situation where you have no way to access more than 1 CPU?
> >>
> >>
> >
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
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Received on Tue Aug 23 2011 - 13:30:04 PDT
