Hi Jason,
Thank you for taking the time to thoroughly explain the REMD system, I'll
have to read more into this simulation method before I work on my own
computations.
Best,
Parker
On Thu, Jul 25, 2013 at 12:17 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Jul 25, 2013 at 9:03 AM, Parker de Waal <Parker.deWaal09.kzoo.edu
> >wrote:
>
> > Hi Amber Users,
> >
> > I'm currently looking into using REMD to simulate the the effects of a
> > single aa substitution and was wondering if anyone had any experience
> with
> > implicit vs explicit solvent models. To my knowledge explicit provides a
> > higher level of accuracy at the expense of increased computational
> demand,
> > however I am unsure how the choice of explicit vs implicit would affect
> the
> > results of REMD.
> >
>
> First off, it's important to realize that REMD, when implemented and used
> properly, samples from exactly the same stationary distributions
> (ensembles) as uncoupled, regular MD simulations run under the exact same
> conditions. The only difference being that replicas can traverse state
> space as well as its standard phase space in order to dodge and/or scale
> high barriers. As a result, the difference between implicit and explicit
> solvent in REMD, as far as sampling and accuracy, is exactly the same as it
> is in standard MD. A simulation run out infinitely long without REMD will
> give exactly the same results as an infinitely long
>
>
> REMD simulation, the only difference being that the REMD simulations
> should converge faster.
>
> The importance of implicit vs. explicit solvent comes from the impact that
> explicit water molecules has on the required number of replicas. For
> T-REMD, specifically, exchange probabilities are calculated via:
>
> Prob = exp(-(Beta_i - Beta_j)*(E_i - E_j))
>
> Therefore, the exchange probability is only high if the temperature and/or
> energy differences are small. The replicas must be spaced such that the
> probability is high enough to give proper mixing (~20% acceptance rate is a
> good target). A good way to see if you will get good exchange rates is to
> look at the overlaps of the energy distributions between adjacent replicas.
> If there is 'good' overlap, then there will be a good chance that exchange
> attempts will occur when the energy difference is small (or, even better,
> negative -- those exchanges are always accepted).
>
> The complication here is that the widths of the energy distributions scales
> as 1/sqrt(N), where N is the number of particles in the system (standard
> stat mech -- look for 'fluctuations' in your favorite text). Thus, as you
> increase the number of particles, the widths of the potential energy
> distributions decreases. This in turn requires that you use more replicas
> spaced closer together in temperature-space to ensure good exchange rates.
> Since explicit solvent simulations tend to have a huge number of particles
> compared to implicit solvent simulations, explicit solvent simulations
> often require many more replicas for T-REMD than do implicit solvent
> calculations to cover the same temperature range. You can play around with
> this link to see the effect of explicit solvent on the number of necessary
> replicas: http://folding.bmc.uu.se/remd/.
>
> Note, this is specific to T-REMD. Other versions of REMD (e.g., pH-REMD
> and umbrella REMD) depend on fluctuations of different variables (like
> total number of titrating protons for pH-REMD and the strength of the
> harmonic restraints for umbrella REMD), so the same arguments do not
> universally apply to "replica exchange" in general.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Jul 26 2013 - 08:00:04 PDT
