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From: Parker de Waal <Parker.deWaal09.kzoo.edu>

Date: Fri, 26 Jul 2013 10:30:56 -0400

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
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Fri Jul 26 2013 - 08:00:04 PDT

Date: Fri, 26 Jul 2013 10:30:56 -0400

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:

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Received on Fri Jul 26 2013 - 08:00:04 PDT

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