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Megha Parashar
,
Jeremy Leung
2
Jan 28
haMSM error
Hi Megha, It's hard to tell exactly what is causing this error just from your output snippet, but
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haMSM error
Hi Megha, It's hard to tell exactly what is causing this error just from your output snippet, but
Jan 28
Isabel Thompson
,
Jeremy Leung
2
Jan 28
Issue with binning at initialization 2D pcoords
Hi Isabel (hope I got your first name right via google search), Recursive bin labels were potentially
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Issue with binning at initialization 2D pcoords
Hi Isabel (hope I got your first name right via google search), Recursive bin labels were potentially
Jan 28
Shashank Shastry
,
Leung, Jeremy
2
Jan 28
Data passing for multiple pcoords
Hi Shashank, Welcome! You are indeed implementing it incorrectly. When passing to $WEST_XXXX_RETURN,
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Data passing for multiple pcoords
Hi Shashank, Welcome! You are indeed implementing it incorrectly. When passing to $WEST_XXXX_RETURN,
Jan 28
Megha Parashar
,
Jeremy Leung
2
Jan 27
bstates and common files in DL-WESTPA
Hi Megha, Welcome to the community! 1. The `bstates/` files are a little different for `DL-enhancedWE
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bstates and common files in DL-WESTPA
Hi Megha, Welcome to the community! 1. The `bstates/` files are a little different for `DL-enhancedWE
Jan 27
Bryan Gworek
,
Leung, Jeremy
3
11/8/25
Restarting corrupt segment
Jeremy, Yes! This was my problem. Thank you for pointing it out, I figured I was missing something.
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Restarting corrupt segment
Jeremy, Yes! This was my problem. Thank you for pointing it out, I figured I was missing something.
11/8/25
Daniel Zuckerman
,
Sunhwan Jo
3
10/20/25
WESTPA Data Club
Sunhwan, we'd be happy to set something up for you. As a reminder, the data club is only
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WESTPA Data Club
Sunhwan, we'd be happy to set something up for you. As a reminder, the data club is only
10/20/25
Harry Ryu
, …
Hayden Scheiber
8
10/13/25
Reassigning $WEST_PCOORD_RETURN outside runseg.sh
Hi everyone, some update on this. Hayden, that is a good suggestion and also what I tried in the
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Reassigning $WEST_PCOORD_RETURN outside runseg.sh
Hi everyone, some update on this. Hayden, that is a good suggestion and also what I tried in the
10/13/25
Schuyler Byrn
, …
Victor Montal Blancafort
5
8/25/25
Multiple GPUs on multiple nodes with zmq and SLURM
Also, thank you Victor for the example script! Best, Schuyler On Fri, Jun 27, 2025 at 4:07 PM Victor
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Multiple GPUs on multiple nodes with zmq and SLURM
Also, thank you Victor for the example script! Best, Schuyler On Fri, Jun 27, 2025 at 4:07 PM Victor
8/25/25
Shashank Shastry
,
Victor Montal Blancafort
3
8/8/25
Running WESTPA2.0 on single GPU
After some tinkering last night, I found that w_run --parallel --n-workers 5 "$@" | tee $
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Running WESTPA2.0 on single GPU
After some tinkering last night, I found that w_run --parallel --n-workers 5 "$@" | tee $
8/8/25
Hayden Scheiber
,
Leung, Jeremy
5
5/30/25
Recycling Trajectories - How are basis state assigned?
Thanks Jeremy, that change in v2022.12 likely resolved the issue. I don't see where any
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Recycling Trajectories - How are basis state assigned?
Thanks Jeremy, that change in v2022.12 likely resolved the issue. I don't see where any
5/30/25
anando...@gmail.com
, …
Victor Montal Blancafort
10
5/2/25
Parallelizing WESTPA + OpenMM on SLURM
Wow, Hayden, really appreciate your detailed answer! Will take a look to everything :) So far I
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Parallelizing WESTPA + OpenMM on SLURM
Wow, Hayden, really appreciate your detailed answer! Will take a look to everything :) So far I
5/2/25
shelby case
, …
Hayden Scheiber
6
5/2/25
Getting Started With Nested Binning Scheme
Hi Shelby, Your westpa configuration binning is still configured for 1D pcoords. In particular, see
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Getting Started With Nested Binning Scheme
Hi Shelby, Your westpa configuration binning is still configured for 1D pcoords. In particular, see
5/2/25
baoyan liu
,
Jeremy Leung
5
4/3/25
Incorrect Binning Behavior of MABBinMapper Scheme
Hi Jeremy, Thank you so much for your kind reply, the illustrative picture, and the recommended paper
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Incorrect Binning Behavior of MABBinMapper Scheme
Hi Jeremy, Thank you so much for your kind reply, the illustrative picture, and the recommended paper
4/3/25
Jeremy Leung
3/18/25
Google Summer of Code 2025 with WESTPA and MDAnalysis
Hi everyone, This year, we've partnered with MDAnalysis on Google Summer of Code. You can help
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Google Summer of Code 2025 with WESTPA and MDAnalysis
Hi everyone, This year, we've partnered with MDAnalysis on Google Summer of Code. You can help
3/18/25
shelby case
,
Jeremy Leung
3
3/6/25
Trouble Storing auxdata in h5
Hi all, Just a small update on the situation for future reference. Shelby was able to identify the
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Trouble Storing auxdata in h5
Hi all, Just a small update on the situation for future reference. Shelby was able to identify the
3/6/25
Anupam Anand Ojha
,
Leung, Jeremy
3
3/5/25
Managing large number of files in WESTPA simulations
Thank you Jeremy for such a quick response. On Wed, Mar 5, 2025 at 1:31 PM 'Leung, Jeremy'
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Managing large number of files in WESTPA simulations
Thank you Jeremy for such a quick response. On Wed, Mar 5, 2025 at 1:31 PM 'Leung, Jeremy'
3/5/25
shelby case
, …
Leung, Jeremy
5
2/10/25
Restarting from Second to Last Iteration and MAB Questions
Thank you, Hayden and Jeremy! This is very helpful! Best, Shelby On Friday, February 7, 2025 at 1:56:
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Restarting from Second to Last Iteration and MAB Questions
Thank you, Hayden and Jeremy! This is very helpful! Best, Shelby On Friday, February 7, 2025 at 1:56:
2/10/25
Praveen Ranganath Prabhakar
,
Goldberg, Alexander
3
2/6/25
tstate definitions for 2D Weighted ensemble
Hi Praveen, You will need to define the target state for both dimensions. For the tstate.file
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tstate definitions for 2D Weighted ensemble
Hi Praveen, You will need to define the target state for both dimensions. For the tstate.file
2/6/25
anando...@gmail.com
,
Jeremy Leung
2
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, Jeremy
3
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
Nell Karpinski
10/31/24
w_bins
Hello WESTPA community, I am using WESTPA/2022.07 and and running the w_bins command. However, this
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w_bins
Hello WESTPA community, I am using WESTPA/2022.07 and and running the w_bins command. However, this
10/31/24
shelby santos
,
Jeremy Leung
2
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
Lillian Chong
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 Leung
5
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 Leung
2
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 Leung
5
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, Jeremy
2
4/29/24
w_ipa Error
Hi Antryg, Sorry for the late reply. I'll address each error message one by one. 1) Sometimes,
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w_ipa Error
Hi Antryg, Sorry for the late reply. I'll address each error message one by one. 1) Sometimes,
4/29/24
Antryg Benedict
,
Jeremy Leung
4
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 Leung
9
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
unread,
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