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1–30 of 337

Welcome to the WESTPA user's mailing list!

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anando...@gmail.com, Jeremy Leung2

12/16/24

WESTPA _OPENMM_2D

Hi Anand, As far as I know, no one worked on that specific configuration. But I suspect it'll be

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WESTPA _OPENMM_2D

Hi Anand, As far as I know, no one worked on that specific configuration. But I suspect it'll be

12/16/24

Yao Fu, Leung, Jeremy3

11/26/24

w_ipa successful trajectories

Hi Jeremy, Thank you for your reply. It works! Best, Yao On Monday, November 25, 2024 at 2:14:45 PM

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w_ipa successful trajectories

Hi Jeremy, Thank you for your reply. It works! Best, Yao On Monday, November 25, 2024 at 2:14:45 PM

11/26/24

10/31/24

Hello WESTPA community, I am using WESTPA/2022.07 and and running the w_bins command. However, this

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Hello WESTPA community, I am using WESTPA/2022.07 and and running the w_bins command. However, this

10/31/24

shelby santos, Jeremy Leung2

9/18/24

Errors with RMSD pcoord

Hi Shelby! You're passing a string as the reference file. You need to open it as a mda.Universe

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Errors with RMSD pcoord

Hi Shelby! You're passing a string as the reference file. You need to open it as a mda.Universe

9/18/24

9/10/24

2024 WESTPA Workshop Tutorials

Dear WESTPA users: We have posted videos of the tutorials offered back in June 2024 for our WESTPA

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2024 WESTPA Workshop Tutorials

Dear WESTPA users: We have posted videos of the tutorials offered back in June 2024 for our WESTPA

9/10/24

Daniel Zuckerman

9/9/24

WESTPA data club availability

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

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WESTPA data club availability

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

9/9/24

Hayden Scheiber, Jeremy Leung5

7/11/24

Making Sense of Number of bins in 2D MAB setup

Hi Hayden, Thanks for the making PR (and fixes)! We'll review it shortly. Cheers, Jeremy L. On

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Making Sense of Number of bins in 2D MAB setup

Hi Hayden, Thanks for the making PR (and fixes)! We'll review it shortly. Cheers, Jeremy L. On

7/11/24

Sangram Prusty, Jeremy Leung2

6/25/24

WESTPA error with init.sh in gromacs 2022.3 NaCl tutorial

Hi Sangram, Please delete line 42 in the west.cfg. We will issue a fix in the near future. Thanks,

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WESTPA error with init.sh in gromacs 2022.3 NaCl tutorial

Hi Sangram, Please delete line 42 in the west.cfg. We will issue a fix in the near future. Thanks,

6/25/24

Chloe Sheen, … Jeremy Leung5

5/8/24

failing to continue next iteration with voronoi bins

Hi Chloe, Unfortunately the WESTPA 1.0 (v2020.XX) installation is structured a little differently and

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failing to continue next iteration with voronoi bins

Hi Chloe, Unfortunately the WESTPA 1.0 (v2020.XX) installation is structured a little differently and

5/8/24

Antryg Benedict, Leung, Jeremy2

4/29/24

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,

4/29/24

Antryg Benedict, Jeremy Leung4

4/16/24

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

4/16/24

Yanxiao Han, Jeremy Leung9

3/20/24

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

3/20/24

Chunzhi Wu, Yang, Darian T5

3/18/24

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

3/18/24

Gabriel Monteiro da Silva, … Harry Ryu6

3/12/24

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

3/12/24

Nell Karpinski, gma572

3/12/24

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

3/12/24

Yanxiao Han, … Lillian Chong4

1/23/24

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

1/23/24

Ashlin James Poruthoor, … Jeremy Leung4

1/16/24

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

1/16/24

Ibrahim Mohamed, … Daniel Zuckerman5

1/12/24

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@

1/12/24

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

unread,

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

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