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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
*

*> >>
*

*> >
*

*> >
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

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

*>
*

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:

-- 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 Sun May 27 2018 - 19:30:02 PDT

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