[gmx-users] REMD temperature spacing error

[Mark Abraham]

People often vary it to try to have an average exchange acceptance rate of
a level they think is useful. But that is only a proxy for what they really
want to achieve, which is replica flow, and it turns out that is a complex
thing and often requires a irregular spacing anyway.

Mark

On Wed, Mar 13, 2013 at 6:02 PM, Nikunj Maheshwari <nixcrazyforher at gmail.com
> wrote:

> Sorry. I thought it was related to Boltzmann constt.
> Then how is 'k' calculated ?
>
> On Wed, Mar 13, 2013 at 8:17 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > k is dimensionless. It does not relate to Boltzmann's constant. The
> > exponential spacing it produces would lead to replica exchange rates that
> > are constant over the T range, under certain assumptions (e.g. papers by
> > David A Kofke). In practice, it normally would not lead to such rates.
> > Whether constant exchange rate is even useful/meaningful is another
> matter
> > (e.g. papers by Walter Nadler & Ulrich Hansmann).
> >
> > Mark
> >
> > On Wed, Mar 13, 2013 at 12:49 PM, Nikunj Maheshwari <
> > nixcrazyforher at gmail.com> wrote:
> >
> > > I think determining k in the equation is not clear. How is it related
> to
> > a
> > > system size? If k=1/(kb.t) [kb=boltzmann constt], then for a given
> > starting
> > > temperature, the temp. spacing will be the same. Is that correct?
> > >
> > > On Wed, Mar 13, 2013 at 5:02 PM, Mark Abraham <
> mark.j.abraham at gmail.com
> > > >wrote:
> > >
> > > > On Wed, Mar 13, 2013 at 11:24 AM, Nikunj Maheshwari <
> > > > nixcrazyforher at gmail.com> wrote:
> > > >
> > > > > Dear all.
> > > > >
> > > > > We are trying to run REMD on two proteins : 292 and 44 aa residues
> > > using
> > > > > GROMACS 4.6.
> > > > > We are unable to obtain the temperature spacing using REMD
> > temperature
> > > > > generator (http://folding.bmc.uu.se/remd/) as it is giving myriad
> > > > > temperature ranges (in the order of 150 for 250-550K range)
> > > > >
> > > >
> > > > Sounds normal for the kind of system you seem to have. Higher numbers
> > of
> > > > degrees of freedom require closer temperature spacing.
> > > >
> > > > Is there any other way to determine the spacing? Can the equation
> > > > > T(i)=T(0).e(k.i) be used, as we are unable to comprehend it?
> > > > >
> > > >
> > > > Yes, but if you want exchanges to occur, there are constraints on the
> > > size
> > > > of k. What's so hard about T(i+1)=T(i)*k?
> > > >
> > > > Mark
> > > > --
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