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From: Jason Swails <jason.swails.gmail.com>

Date: Wed, 05 Nov 2014 12:05:07 -0500

On Wed, 2014-11-05 at 16:20 +0000, Mele N. wrote:

*> Dear Amber user,
*

*>
*

*> I am currently using Temperature REMD simulation and I would like to
*

*> use H-REMD to improve my knowledge.
*

*>
*

*> However, I can't understand how to perform H-REMD in AMBER. With
*

*> T-REMD we specify as an input file a set of temperatures (generated by
*

*> gromacs generator in my case) so I would like to understand how do we
*

*> choose the number of replicas?
*

Guesstimate. Run a short simulation and take a look at the exchange

acceptance rates and adjust your replica number (and/or spacing) based

on the results.

Note that T-REMD is rather unique in this regard. The replica spacing

comes from potential energy distributions, whose fluctuations (i.e., the

width of the potential energy distributions) are based in statistical

mechanics and vary inversely with the square root of the number of

particles. I think there may be _some_ empiricism in the formula the

GROMACS temperature generator uses, but at the end of the day you can

get a pretty good prediction of the exchange probabilities based on just

the number of degrees of freedom in your system.

There is no analog to this in H-REMD, where acceptance rates in state

space depend on the complex nature of the underlying Hamiltonian and

exchange dimension. What's more, the shape of the underlying free

energy surface in state space is not the same (or even similar) for

every system, so the "optimum" replica number and spacing you choose for

one system is not necessarily transferable to another. (Note that

"optimum" here can have different exact definitions, but that does not

affect the validity of my statement).

Consider an umbrella replica exchange simulation -- the umbrella

coordinate distributions will be far narrower in regions near the

transition state where the free energy surface is the steepest, so you

will need more replicas in that region to avoid introducing a bottleneck

in state space sampling.

*> I tried to find paper or tutorial on it but I couldn't managed, if you
*

*> have any advices it would be appreciated.
*

Have a look at http://pubs.acs.org/doi/abs/10.1021/ct400366h. While

this paper doesn't answer your exact question and is specific to

umbrella sampling, it should help yield some of the insight needed to

figure it out yourself. It should also be possible, if not

straightforward, to extend these ideas to other forms of replica

exchange (like alchemical replica exchange free energy perturbation,

pH-replica exchange, etc.)

Another way of thinking about this is that you need _some_ knowledge of

the underlying surface in state space in order to pick the "best"

locations for your replicas (as well as how many replicas will be

needed). With T-REMD, you have knowledge a priori of what this surface

looks like. With H-REMD, in the most general case, you do not. The

best way to estimate the shape of that surface is to start with your

best guess of where you should put replicas and just give it a try.

HTH,

Jason

Date: Wed, 05 Nov 2014 12:05:07 -0500

On Wed, 2014-11-05 at 16:20 +0000, Mele N. wrote:

Guesstimate. Run a short simulation and take a look at the exchange

acceptance rates and adjust your replica number (and/or spacing) based

on the results.

Note that T-REMD is rather unique in this regard. The replica spacing

comes from potential energy distributions, whose fluctuations (i.e., the

width of the potential energy distributions) are based in statistical

mechanics and vary inversely with the square root of the number of

particles. I think there may be _some_ empiricism in the formula the

GROMACS temperature generator uses, but at the end of the day you can

get a pretty good prediction of the exchange probabilities based on just

the number of degrees of freedom in your system.

There is no analog to this in H-REMD, where acceptance rates in state

space depend on the complex nature of the underlying Hamiltonian and

exchange dimension. What's more, the shape of the underlying free

energy surface in state space is not the same (or even similar) for

every system, so the "optimum" replica number and spacing you choose for

one system is not necessarily transferable to another. (Note that

"optimum" here can have different exact definitions, but that does not

affect the validity of my statement).

Consider an umbrella replica exchange simulation -- the umbrella

coordinate distributions will be far narrower in regions near the

transition state where the free energy surface is the steepest, so you

will need more replicas in that region to avoid introducing a bottleneck

in state space sampling.

Have a look at http://pubs.acs.org/doi/abs/10.1021/ct400366h. While

this paper doesn't answer your exact question and is specific to

umbrella sampling, it should help yield some of the insight needed to

figure it out yourself. It should also be possible, if not

straightforward, to extend these ideas to other forms of replica

exchange (like alchemical replica exchange free energy perturbation,

pH-replica exchange, etc.)

Another way of thinking about this is that you need _some_ knowledge of

the underlying surface in state space in order to pick the "best"

locations for your replicas (as well as how many replicas will be

needed). With T-REMD, you have knowledge a priori of what this surface

looks like. With H-REMD, in the most general case, you do not. The

best way to estimate the shape of that surface is to start with your

best guess of where you should put replicas and just give it a try.

HTH,

Jason

-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Nov 05 2014 - 09:30:03 PST

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