is the analysis section in west.cfg of tutorial 7.3 correct?

[Ibrahim Mohamed]

i was following the tutorial 7.3 and found that the analysis section contains these boundaries  [0.0,2.6,12.0,'inf']. Should not they be [0.0,4.0,'inf'] since the folded state is within 0 and 4.0 and unfolded state is larger than 4.0?


analysis:

     directory: ANALYSIS                # specify the directory all analysis files should exist in.

     kinetics:                          # general options for both kinetics routines.

       step_iter: 1

       evolution: cumulative

       extra: [ 'disable-correl' ]

     analysis_schemes:                  # Analysis schemes.  Required: name (TEST), states, and bins

       TEST:

         enabled: True

         bins:

           - type: RectilinearBinMapper

             boundaries:

               - [0.0,2.6,12.0,'inf']

         states:

           - label: bound

             coords:

               - [0]

           - label: unbound

             coords:

               - [12.1]  

[Ford, Baily Wayne]

Hi Ibrahim,

The boundaries listed here are just place holders from the NaCl simulations; they have since been removed to avoid confusion. Tutorial 7.3 is intended to familiarize users with alternative methods for calculating rates, so w_ipa is not advised. For tutorial 7.3, it is recommended to use the w_fluxanl tool to generate a fluxanl.h5 file that contains the instantaneous probability flux into the target state for each iteration. From there, you can use the supplied get_mean_rate.py script with the appropriate Tau value and time width to calculate rate constants. 

Best,

Baily Ford

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From: westpa...@googlegroups.com <westpa...@googlegroups.com> on behalf of Ibrahim Mohamed <hollowic...@gmail.com>
Sent: Monday, October 23, 2023 8:39 AM
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Subject: [westpa-users] is the analysis section in west.cfg of tutorial 7.3 correct?

 

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[hollowic...@gmail.com]

Hi Baily,

Thank you for your description. i have not finished the tutorial yet so i did not know that w_ipa will not be used.
So this mean that whether this section is present or not the rest of the tutorial will not depend on it, right?

Thanks

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[Ford, Baily Wayne]

Hi Ibrahim, 

All of 7.3 should be independent of the analysis section in the west.cfg file. Feel free to remove it if you wish, but if shouldn't cause any issue if you just ignore it.

I hope this helps,

Baily Ford

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Sent: Monday, October 23, 2023 2:59 PM
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Subject: Re: [westpa-users] is the analysis section in west.cfg of tutorial 7.3 correct?

 

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[hollowic...@gmail.com]

Is it possible to have a negative inf value in the boundaries? 

For example can I have these boundary [inf, 20,15,10,5,0,-5,-10,-15,-20, -inf] in West.cfg file

Thanks

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[Nicolas Frazee]

Hey Ibrahim,

The bins must be set to be increasing from negative to positive. Negative infinity can be defined but must be surrounded by quotes: '-inf'

['-inf', -20, -15, -10, -5, ...]

Nick