[gmx-users] REMD Showing Zero Exchange Probability
lichuligesh at gmail.com
Wed Jul 25 07:57:19 CEST 2018
Sorry for the delay..Thank you Mark..
On Sat, Jul 21, 2018 at 2:09 AM, Mark Abraham <mark.j.abraham at gmail.com>
> You can't arbitrarily choose both the temperature range and number of
> replicas and get non-zero exchange probability. See
> https://pubs.acs.org/action/showCitFormats?doi=10.1021%2Fct800016r. For a
> given average exchange probability, choose a range and thus the number of
> replicas, or the number of replicas and thus the range.
> On Fri, Jul 20, 2018, 10:39 Ligesh Lichu <lichuligesh at gmail.com> wrote:
> > Dear all,
> > I have performed REMD for a system containing Protein, Reline, Urea
> > 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
> > 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
> > some temperatures in between?
> > If I am using the equation *Ti = T0 exp (k* i)*, what determines the
> > of 'k' how it affects the exchange probability? How can I choose the
> > of 'k' for an arbitrary system?
> > Thanks in advance...
> > --
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