Thanks for the guidance!
Sophia
On Mon, Oct 25, 2010 at 7:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Sun, Oct 24, 2010 at 8:01 PM, Cheng-I Lee <biocil.ccu.edu.tw> wrote:
> >
> > 1. Equilibration: how to judge if the duration of the equilibration is
> long
> > enough? In the Amber tutorials (A7), 200 ps of equilibration was
> performed.
> > Is 200 ps of simulation usually good enough?
>
> The answer is really going to be system-dependent. Keep in mind that
> reaching true equilibirum with your system can be really difficult to
> do - what the tutorial refers to is really more of an extension of
> minimization to get each replica to a target temperature. For your
> simulation just keep an eye on the thermodynamic properties of the
> system (at the very least the potential energy and temperature, and
> for explicit solvent definitely keep track of the density as well).
> Once the running averages and fluctuations start to look like they
> aren't changing very much the system is probably OK for future runs,
> but keep in mind this still might not be true equilibrium. With
> replica exchange you can usually get away with running brief MD like
> this to get your replicas to their target temperatures and then rely
> on the exchanges themselves to drive you to equilibirum. In that case
> just keep in mind that part of your "production run" is really just
> equilibration. Note that the tutorial in question is for a quite small
> (109 atom) system in implicit solvent; for larger systems more than
> 200 ps will certainly be needed.
>
> >
> > 2. In replica exchange, how many times of exchange should I expect?
>
> Unfortunately there's no rule for this either; you should exchange for
> as many times as it takes to see whatever you are hoping to see. You
> may also want to read this article for a discussion about how often to
> exchange ("Exchange frequency in replica exchange molecular dynamics."
> D. Sindhikara et al. J. Chem. Phys. 128, 024103 (2008)).
>
> Hope this helps.
>
> -Dan
>
> >
> > Thanks for the help!
> >
> > Sophia
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Received on Mon Oct 25 2010 - 05:30:05 PDT
