# Re: [AMBER] ABMD with multiple walkers

From: Feng Pan <fpan3.ncsu.edu>
Date: Mon, 28 May 2018 21:01:21 -0400

Leading to 0 walker means this replica will be removed, replaced by another
replica which leads to 2 walkers.

Leading to 1 walker means the walker will stay with itself, but the index
may
shift to the next one when it has neighboring replica leading to 0 walkers.

When it is converged, each replica should lead to 1 walker, which means
the selection actually does not take effects.

Feng

On Mon, May 28, 2018 at 8:36 AM, Qinghua Liao <scorpio.liao.gmail.com>
wrote:

> Hello Feng,
>
>
> A few more questions:
>
> Leading to 0 walker means that the walker will be stayed with itself or
> copied by another walker
> which leads to 2 walkers?
> Leading to 1 walker means that this walker might be stayed with itself or
> can copied by another walker which leads to 1 walker too?
>
> What would be the selection scores of all walkers if the ABMD with
> multiple walkers is converged?
>
> Thanks so much!
>
>
> All the best,
> Qinghua
>
>
>
> On 05/28/2018 04:05 AM, Feng Pan wrote:
> > 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
> >>>>
> >>>
> >>
> >> _______________________________________________
> >> AMBER mailing list
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> >>
> >
> >
>
>
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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 Mon May 28 2018 - 18:30:02 PDT
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