[gmx-users] REMD Showing Zero Exchange Probability

[Ligesh Lichu]

Sorry for the delay..Thank you Mark..

On Sat, Jul 21, 2018 at 2:09 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> 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.
>
> Mark
>
> 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...
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>