# Re: [AMBER] ABMD with multiple walkers

From: Feng Pan <fpan3.ncsu.edu>
Date: Sun, 27 May 2018 22:05:45 -0400

Hi, Qinghua

Yes, you are right, I made a mistake. I check the codes. A random number
between 0 to 1/8
should be added to the score.
For example, for the first replica, if the sum is below 1/8 (like the score
is below 1/8 and
the random number is also small), this replica leads to zero walkers. If
the sum is between
1/8 and 2/8, leads to 1 walker. The following replicas will be calculated
to make sure the
total number of walkers is 8.
So basically when you see the score is below 1/8, the walker could be 0 or
1.

When I say walkers will be copied, I mean the coordinates
will be copied.

Best
Feng

On Sun, May 27, 2018 at 5:08 PM, Qinghua Liao <scorpio.liao.gmail.com>
wrote:

> Dear Feng,
>
> Thanks a lot for your explanation.
>
> Following your explanation, I also found that there are some walkers
> which have the scores
> between 1/8 and 2/8, but the walkers were not copied to 2 walkers.
>
> When the score is less than 1/8, the walker will be kept itself, then
> the sign is "=> 0" or "=> 1"
>
> About the term "walkers will be copied", are coordinates copied or
> selection score (weight)? Thanks a lot!
>
>
> All the best,
> Qinghua
>
> On 05/27/2018 04:16 AM, Feng Pan wrote:
> > Hi, Qinghua
> >
> > the selection score is the ratio of the replica selection weight over the
> > total weight,
> > so if you have 8 replicas here, and the score is below 1/8, the walker
> will
> > keep
> > itself. If the score is between 1/8 and 2/8, the walker will be copied
> to 2
> > walkers, as
> > shown like => 2 walkers.
> >
> > When the entropy is above the threshold, the selection will be
> calculated,
> > but if
> > every selection score is below 1/8, there will be no resampling, every
> > walker will
> > be kept just itself.
> >
> > Best
> > Feng
> >
> > On Fri, May 25, 2018 at 7:00 PM, Qinghua Liao <scorpio.liao.gmail.com>
> > wrote:
> >
> >> Hello Amber developers,
> >>
> >> Currently, I am running ABMD with multiple walkers, but I have some
> >> questions regarding interpreting the output.
> >> Here is my input for the multiple walkers:
> >>
> >> selection_freq = 500
> >> selection_constant = 0.00001
> >> selection_epsilon = 0.0
> >>
> >> And here are some output from the simulations:
> >> #
> >> NFE : selection score for walker 1 is 0.930991 / 7.992304 = 0.116 =>
> 0
> >> walker(s)
> >> NFE : selection score for walker 2 is 0.881570 / 7.992304 = 0.110 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 3 is 0.945704 / 7.992304 = 0.118 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 4 is 0.951837 / 7.992304 = 0.119 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 5 is 0.973335 / 7.992304 = 0.122 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 6 is 1.103148 / 7.992304 = 0.138 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 7 is 0.967854 / 7.992304 = 0.121 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 8 is 1.237866 / 7.992304 = 0.155 =>
> 2
> >> walker(s)
> >> NFE : Selection entropy 0.005597 is greater than threshold 0.000000
> >> NFE : Selection resampling : new 1 comes from 2
> >> #
> >> #
> >> NFE : selection score for walker 1 is 1.042757 / 7.817606 = 0.133 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 2 is 0.956335 / 7.817606 = 0.122 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 3 is 0.775833 / 7.817606 = 0.099 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 4 is 0.906343 / 7.817606 = 0.116 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 5 is 0.938005 / 7.817606 = 0.120 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 6 is 0.851424 / 7.817606 = 0.109 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 7 is 1.232238 / 7.817606 = 0.158 =>
> 1
> >> walker(s)
> >> NFE : selection score for walker 8 is 1.114672 / 7.817606 = 0.143 =>
> 1
> >> walker(s)
> >> NFE : Selection entropy 0.009795 is greater than threshold 0.000000
> >> #
> >>
> >> How should I understand the selection score, how is it calculated? What
> >> does "=>0 (1,2) walker(s)" mean?
> >> For the first assessment, the selection entropy is 0.005597,
> >> which is greater than the threshold 0.0, and then there is a selection
> >> resampling (new 1 comes from 2). For the second
> >> assessment, the selection entropy is also greater than the threshold,
> >> but there is no resampling. Why is this different?
> >>
> >> I appreciate any of your responds.
> >>
> >>
> >> All the best,
> >> Qinghua
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
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>

```--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email:  fpan3.ncsu.edu
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Received on Sun May 27 2018 - 19:30:02 PDT
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