[gmx-users] REMD Showing Zero Exchange Probability
mark.j.abraham at gmail.com
Fri Jul 20 22:39:50 CEST 2018
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 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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