[gmx-users] REMD Showing Zero Exchange Probability

[Abhishek Acharya]

Hello,

The REMD generator provides an estimate of the number of replicas that may
be necessary (based on the system size) for performing replica exchange
properly. Since you got 47 replicas, you can maybe play around with
replicas more or less around that range. Maybe 16 replicas is much less for
your system. You can check whether the energy distributions obtained from
the replicas overlap properly or not.

If your system is such that you can make do with sampling a smaller
subspace of your system, then perhaps REST2 (Replica Exchange with Solute
Scaling, IIRC) may be be helpful. Although, I haven't come across many
articles lately that have used it. I would also suggest you explore other
sampling methods and see if they can be adapted to your problem of interest.

Best Regards,
Abhishek


On Fri, Jul 20, 2018 at 5:55 PM, Ligesh Lichu <lichuligesh at gmail.com> wrote:

> I have tried an exchange every 2 ps. That is every 1000 steps.
>
> On Fri, Jul 20, 2018 at 5:34 PM, Smith, Micholas D. <smithmd at ornl.gov>
> wrote:
>
> > How frequently are you trying to exchange?
> >
> > ===================
> > Micholas Dean Smith, PhD. MRSC
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Ligesh
> > Lichu <lichuligesh at gmail.com>
> > Sent: Friday, July 20, 2018 4:39 AM
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] REMD Showing Zero Exchange Probability
> >
> > Dear all,
> >     I have performed REMD for a system containing Protein, Reline, Urea
> and
> > Water in the temperature range 290 to 450 K consist of 16 replicas out of
> > 47 replicas generated by REMD temperature generator. But after the MD
> > simulation the exchange probability is zero. I have used position
> > restraints for reline, urea and protein. Is there any chance that
> position
> > restraints  cause the exchange probability to be zero?  I have one more
> > query that, the REMD temperature generator produced around 45 to 54
> > replicas for my system in the required temperature range. But I have only
> > 80 processors to do the job, So is it necessary to choose the consecutive
> > temperature replicas given by the REMD temperature generator or I can
> skip
> > some temperatures in between?
> >
> > If I am using the equation *Ti = T0 exp (k* i)*, what determines the
> value
> > of 'k'  how it affects the exchange probability? How can I choose the
> value
> > of 'k' for an arbitrary system?
> >
> > Thanks in advance...
> > --
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