note also that if you want to use constant pressure, consider the fact that
most people use REMD temperature ranges that extend above the boiling point
of water at 1atm.
On Thu, Mar 14, 2013 at 7:43 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Mar 14, 2013 at 7:07 PM, sudipta <sudipta.mml.gmail.com> wrote:
>
> > Hi Niel,
> >
> > Thank you very much for your reply. Yeah, I noticed that most of the
> people
> > had used NVT instead of NPT. Nobody has not put any straightforward
> reason
> > for choosing NVT over NPT.
>
>
> Convenience and simplicity. The exchange probability is currently
> calculated from basically a ratio of Boltzmann probabilities between the
> two states in adjacent replicas. Boltzmann probabilities are valid for
> NVT, only. To support NPT with REMD, a PV term needs to be added, I think.
>
>
> > However, is the simulation of protein system at
> > high temperature in NVT ensemble reasonable? When we increase the
> > temperature of such system then the protein molecule will be expanded and
> > it looks for some space. However, NVT ensemble doesn't compromise any
> > space. I am curious about this.
> >
>
> When fluctuations are not important, all ensembles are effectively
> identical. It is only when these fluctuations begin to become large (at,
> for instance, phase transitions), that you need to be careful about your
> ensemble. However, the purpose of the high-temperature replicas is NOT to
> see how the system behaves at that temperature. In fact, many T-REMD
> simulations have replicas at temperatures over the boiling point of water
> at 1 bar.
>
> To properly model this behavior, you would naturally need to use NPT... but
> you don't want to model the behavior of boiling proteins (if you did, then
> a force field parametrized at 300K is _not_ the way to go). The only
> purpose of using high-temperature replicas is to generate a series of
> structures that 'might' be relevant at a lower temperature that are hard to
> reach there due to large barriers in phase space.
>
> The fact that high-temperature replicas are nonsensical due to the force
> field not being validated at such temperatures as well as the issues you
> raise due to our choice of ensemble are actually irrelevant. Because the
> exchange probability obeys detailed balance, you are assured that your
> low-temperature replicas are thermodynamically correct. The
> high-temperature replicas are used only to enhance sampling and serve
> little use after the simulation is over (you can use them for some stuff,
> like reweighting, but are often just discarded).
>
> In fact, if you ran NPT, then you would actually _hurt_ your exchange
> success rate if you came anywhere close to the boiling point of water,
> since the volume would expand too much. So IMO, NVT is the better choice
> for most REMD simulations.
>
> Another issue is use of explicit solvent. Most of REMD study has been
> > performed in implicit solvent environment. Is there any inherent reason
> > behind this except computational cost.
> >
>
> Computational cost is the only reason. But the computational cost
> increases for two reasons. First, more particles means slower simulations,
> and the viscosity of water molecules hinders conformational sampling in
> explicit solvent compared to implicit solvent -- so you need longer
> simulations that run slower.
>
> Even worse with REMD, though, is that the width of your potential energy
> distribution scales as 1/sqrt(N) where N is the # of particles. With
> explicit solvent (or any large system), the number of particles becomes
> large, so the potential energy distributions become narrow. Since these
> distributions must overlap in order for REMD to be effective, you need to
> place replicas much closer together. Therefore, in order to span the same
> temperature range in explicit solvent, you often need many, many more
> replicas.
>
> That is why T-REMD simulations are typically (although not always) run with
> implicit solvent unless the system size is rather small to begin with.
> (e.g., alanine dipeptide)
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Fri Mar 15 2013 - 09:30:02 PDT
