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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,
*

*>
*

*> Thanks a lot for your reply.
*

*>
*

*> 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
*

*> >> AMBER.ambermd.org
*

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

*> >>
*

*> >
*

*> >
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

*>
*

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:

-- Feng Pan Ph.D. North Carolina State University Department of Physics Email: fpan3.ncsu.edu _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon May 28 2018 - 18:30:02 PDT

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