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Welcome to the WESTPA user's mailing list!

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May 3

failing to continue next iteration with voronoi bins

Hello WESTPA users, I'm trying to use the VoronoiBinMapper along with the string method (westext.

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failing to continue next iteration with voronoi bins

Hello WESTPA users, I'm trying to use the VoronoiBinMapper along with the string method (westext.

May 3

Antryg Benedict, Leung, Jeremy2

Apr 29

Hi Antryg, Sorry for the late reply. I'll address each error message one by one. 1) Sometimes,

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Hi Antryg, Sorry for the late reply. I'll address each error message one by one. 1) Sometimes,

Apr 29

Antryg Benedict, Jeremy Leung4

Apr 16

WESTPA Error with init.sh

Hi Antryg, v2022.08 should be on PyPI and most of the builds should be on conda. (Anaconda servers

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WESTPA Error with init.sh

Hi Antryg, v2022.08 should be on PyPI and most of the builds should be on conda. (Anaconda servers

Apr 16

Yanxiao Han, Jeremy Leung9

Mar 20

LPATH, Linguistics Pathway Analysis of Trajectories using Hierarchical clustering

Hi Jeremy, Thank you for your help. The problems were resolved. Thank you for your suggestions for

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LPATH, Linguistics Pathway Analysis of Trajectories using Hierarchical clustering

Hi Jeremy, Thank you for your help. The problems were resolved. Thank you for your suggestions for

Mar 20

Chunzhi Wu, Yang, Darian T5

Mar 18

How to run WESS after regular WE iterations

Thanks Darian! I fixed the indent and now it's working. On Monday, March 18, 2024 at 6:12:37 PM

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How to run WESS after regular WE iterations

Thanks Darian! I fixed the indent and now it's working. On Monday, March 18, 2024 at 6:12:37 PM

Mar 18

Gabriel Monteiro da Silva, … Harry Ryu6

Mar 12

Steps to apply haMSM restarting to a simulation that ran with the MABB scheme?

Gotcha, sounds good. The script can be found here: https://github.com/wryu94/haMSM_script/tree/main

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Steps to apply haMSM restarting to a simulation that ran with the MABB scheme?

Gotcha, sounds good. The script can be found here: https://github.com/wryu94/haMSM_script/tree/main

Mar 12

Nell Karpinski, gma572

Mar 12

Question about w_bins & progress coordinate values

Hi Nell, Thank you for your question! The w_bins command reports bin occupancy at the first frame of

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Question about w_bins & progress coordinate values

Hi Nell, Thank you for your question! The w_bins command reports bin occupancy at the first frame of

Mar 12

Yanxiao Han, … Lillian Chong4

Jan 23

Thank you so much Dan and Lillian for offering help. I will talk to my PI about this. Meanwhile, I

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Thank you so much Dan and Lillian for offering help. I will talk to my PI about this. Meanwhile, I

Jan 23

Ashlin James Poruthoor, … Jeremy Leung4

Jan 16

Traj reading goes silently rogue for big systems

Hi Lillian and Jeremy, Thank you for your input. I will post this as a GH issue and discuss it over

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Traj reading goes silently rogue for big systems

Hi Lillian and Jeremy, Thank you for your input. I will post this as a GH issue and discuss it over

Jan 16

Ibrahim Mohamed, … Daniel Zuckerman5

Jan 12

Question about the usage of GPUs

Hayden, thanks. You make a good point. --Dan From: westpa...@googlegroups.com <westpa-users@

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Question about the usage of GPUs

Hayden, thanks. You make a good point. --Dan From: westpa...@googlegroups.com <westpa-users@

Jan 12

Jonathan Borowsky, Jeremy Leung8

12/5/23

initialization error with haMSM simulations

Hi Jeremy, Thank you so much for all the help! I'll read up on steady state simulations and

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initialization error with haMSM simulations

Hi Jeremy, Thank you so much for all the help! I'll read up on steady state simulations and

12/5/23

Ibrahim Mohamed, … Yang, Darian T3

12/3/23

Is it correct to convert from a steady state WE to equilibrium WE if no segment reached the target state?

Ibrahim, You can use w_init if you're starting a new simulation, thus generating a new h5 file

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Is it correct to convert from a steady state WE to equilibrium WE if no segment reached the target state?

Ibrahim, You can use w_init if you're starting a new simulation, thus generating a new h5 file

12/3/23

Ehsan Mirafzali, Anthony Bogetti2

12/3/23

Seeking Assistance for Creating Full Trajectory Movies from Tutorials 7.2 and 7.3

Hello, Create full trajectory movies in WESTPA 2.0 can be accomplished with the westpa.analysis

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Seeking Assistance for Creating Full Trajectory Movies from Tutorials 7.2 and 7.3

Hello, Create full trajectory movies in WESTPA 2.0 can be accomplished with the westpa.analysis

12/3/23

Hayden Scheiber, … Lillian Chong12

11/28/23

haMSMs with progress coordinates?

Hi Hayden, I hope you had a nice Thanksgiving! We are just getting back into things after the

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haMSMs with progress coordinates?

Hi Hayden, I hope you had a nice Thanksgiving! We are just getting back into things after the

11/28/23

Maciej, Leung, Jeremy3

11/22/23

error in tutorial 7.1 - (Na Cl association)

Hi Jeremy, Thank you for your advice. Indeed there was a problem with md simulation in segment 30.

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error in tutorial 7.1 - (Na Cl association)

Hi Jeremy, Thank you for your advice. Indeed there was a problem with md simulation in segment 30.

11/22/23

Hayden Scheiber, Anthony Bogetti3

11/15/23

MAB skipping function: still broken in v2022.6?

Hi Anthony, Glad to hear you are working on resolving this bug. It's not a major problem for my

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MAB skipping function: still broken in v2022.6?

Hi Anthony, Glad to hear you are working on resolving this bug. It's not a major problem for my

11/15/23

Ibrahim Mohamed, Jeremy Leung16

11/14/23

How can i repeat a we iteration after removing it?

Okay thank you for this suggestion. Yahoo Mail: Search, organise, conquer On Mon, 13 Nov 2023 at 11:

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How can i repeat a we iteration after removing it?

Okay thank you for this suggestion. Yahoo Mail: Search, organise, conquer On Mon, 13 Nov 2023 at 11:

11/14/23

Chloe Sheen, Jeremy Leung2

11/13/23

issues using w_ipa

Hi Chloe, When you're defining states, each bullet point should be [1st dim, 2nd dim] to specify

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issues using w_ipa

Hi Chloe, When you're defining states, each bullet point should be [1st dim, 2nd dim] to specify

11/13/23

Daniel Zuckerman

11/1/23

I want to remind everyone about the availability of the WESTPA 'data club'. The data club is

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I want to remind everyone about the availability of the WESTPA 'data club'. The data club is

11/1/23

Ibrahim Mohamed, … Nicolas Frazee6

10/30/23

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

Hey Ibrahim, The bins must be set to be increasing from negative to positive. Negative infinity can

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

Hey Ibrahim, The bins must be set to be increasing from negative to positive. Negative infinity can

10/30/23

Jonathan Borowsky, Jeremy Leung5

10/23/23

MAB bin boundaries (WESTPA 2.0)

Hi Jeremy, Thank you for adding the feature and for letting me know! Best, Jonathan On Friday,

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MAB bin boundaries (WESTPA 2.0)

Hi Jeremy, Thank you for adding the feature and for letting me know! Best, Jonathan On Friday,

10/23/23

Ibrahim Mohamed, Nicolas Frazee3

10/19/23

error while continuing the WE

Sorry, I forgot that you'll also need to remove the `iter_000037.h5` from your `traj_segs`

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error while continuing the WE

Sorry, I forgot that you'll also need to remove the `iter_000037.h5` from your `traj_segs`

10/19/23

Mac Kevin Braza, … Yang, Darian T6

10/3/23

Hey Kevin, Thanks a lot for giving wedap a try and for letting us know about this issue! And thanks

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Hey Kevin, Thanks a lot for giving wedap a try and for letting us know about this issue! And thanks

10/3/23

Ibrahim Mohamed, Nicolas Frazee2

10/3/23

is it right to remove the not needed files while westpa is running?

Hello! Thanks for the question. It is safe to remove the files from the current iteration - 2 in

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is it right to remove the not needed files while westpa is running?

Hello! Thanks for the question. It is safe to remove the files from the current iteration - 2 in

10/3/23

Hayden Scheiber, … Jeremy Leung16

9/27/23

Westpa HDF5 Framework with GROMACS?

Hi Jeremy, I did some testing to pinpoint exactly when the seg faults occur. Below is what I found. I

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Westpa HDF5 Framework with GROMACS?

Hi Jeremy, I did some testing to pinpoint exactly when the seg faults occur. Below is what I found. I

9/27/23

Hayden Scheiber, Leung, Jeremy5

9/25/23

Accessing restart files in HDF5 framework outside of WESTPA?

Awesome, that works. Thanks Jeremy! On Friday, September 22, 2023 at 5:34:49 PM UTC-7 jml...@pitt.edu

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Accessing restart files in HDF5 framework outside of WESTPA?

Awesome, that works. Thanks Jeremy! On Friday, September 22, 2023 at 5:34:49 PM UTC-7 jml...@pitt.edu

9/25/23

Ibrahim Mohamed, Jeremy Leung6

9/22/23

ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject error

okay thank you for your advice. actually the problem was that after i activate the WESTPA environment

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ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject error

okay thank you for your advice. actually the problem was that after i activate the WESTPA environment

9/22/23

Ibrahim Mohamed, … Yang, Darian T14

9/15/23

error values in the target flux evolution

Hi Ibrahim, I agree that it seems likely to come down to the hdfview, we have actually come into a

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error values in the target flux evolution

Hi Ibrahim, I agree that it seems likely to come down to the hdfview, we have actually come into a

9/15/23

Ibrahim Mohamed, Leung, Jeremy4

9/5/23

getting the trajectory from tracing a walker

Hi Ibrahim, Let me answer in order. 1. Yes. The whole problem with loading with westpa.analysis is

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getting the trajectory from tracing a walker

Hi Ibrahim, Let me answer in order. 1. Yes. The whole problem with loading with westpa.analysis is

9/5/23

Ibrahim Mohamed, Lillian Chong2

9/4/23

is it correct to use the leap frog integrator in GROMACS with WESTPA?

Ibrahim, WE simulation requires the use of stochastic dynamics. For MD simulations, this is typically

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is it correct to use the leap frog integrator in GROMACS with WESTPA?

Ibrahim, WE simulation requires the use of stochastic dynamics. For MD simulations, this is typically

9/4/23

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