westpa-users

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Fernando Amrein, … Leung, Jeremy16

Mar 21

Having difficulty with the AMBER NaCl tutorial. Getting errors and not sure how to source amber to do calculations.

Disregard the last two messages, it is working now. Thanks! On Tue, 21 Mar 2023 at 15:11, Fernando

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Having difficulty with the AMBER NaCl tutorial. Getting errors and not sure how to source amber to do calculations.

Disregard the last two messages, it is working now. Thanks! On Tue, 21 Mar 2023 at 15:11, Fernando

Mar 21

Gabriel Monteiro da Silva, Lillian Chong3

Mar 3

Using different topologies for different starting states

That makes sense, I forgot about the potential for PBC artifacts from having too narrow a box in a

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Using different topologies for different starting states

That makes sense, I forgot about the potential for PBC artifacts from having too narrow a box in a

Mar 3

Eduardo Jardón, Anthony Bogetti2

Feb 15

Fwd: w_run --oneseg

Hello Eduardo, The best way to re-run those segments is to “truncate” your h5 datafile to a previous

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Fwd: w_run --oneseg

Hello Eduardo, The best way to re-run those segments is to “truncate” your h5 datafile to a previous

Feb 15

Chloe Sheen, … Leung, Jeremy3

Jan 27

Question about calculating MFPT

Hi Chloe, Regarding the variable names, indeed `trajlabels` would be what you want to be using for

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Question about calculating MFPT

Hi Chloe, Regarding the variable names, indeed `trajlabels` would be what you want to be using for

Jan 27

Razvan Marinescu, … Anthony Bogetti6

Jan 16

OverflowError: cannot convert float infinity to integer

Thank you both! I'll try that. -R On Monday, 16 January 2023 at 10:31:00 UTC-8 Anthony Bogetti

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OverflowError: cannot convert float infinity to integer

Thank you both! I'll try that. -R On Monday, 16 January 2023 at 10:31:00 UTC-8 Anthony Bogetti

Jan 16

Razvan Marinescu, … Razvan Marinescu12

Jan 15

Time taken by WESTPA iteration doesn't match simulation length

Hi Jeremy and Antony, That is great, thank you very much! Do you also have a script that traces out a

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Time taken by WESTPA iteration doesn't match simulation length

Hi Jeremy and Antony, That is great, thank you very much! Do you also have a script that traces out a

Jan 15

Razvan Marinescu2

Jan 13

Error when running with ZMQ on cluster: no workers available

Never mind. I just found the problem, there was an error when computing the progress coordinates in

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Error when running with ZMQ on cluster: no workers available

Never mind. I just found the problem, there was an error when computing the progress coordinates in

Jan 13

jintu zhang, … Leung, Jeremy7

12/20/22

Question about the `total_flux` dataset in the direct.h5 file.

Dear Jeremy, Thank you very much for the answers! These are really helpful. Jintu Zhang 在2022年12月17日

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Question about the `total_flux` dataset in the direct.h5 file.

Dear Jeremy, Thank you very much for the answers! These are really helpful. Jintu Zhang 在2022年12月17日

12/20/22

Chloe Sheen, Leung, Jeremy4

12/17/22

Running basic_nacl_group_by_color tutorial

Hi Chloe, You're correct that the problem stems from WESTPA v2020.05 (ie WESTPA 1.0). Subgroups

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Running basic_nacl_group_by_color tutorial

Hi Chloe, You're correct that the problem stems from WESTPA v2020.05 (ie WESTPA 1.0). Subgroups

12/17/22

Paween Mahinthichaichan, … Leung, Jeremy4

12/16/22

reconstructing PMF from CVs other than progress coordinate

Hi Paween, In addition to what Dr. Zuckerman has posted, here's advice on the technical side of

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reconstructing PMF from CVs other than progress coordinate

Hi Paween, In addition to what Dr. Zuckerman has posted, here's advice on the technical side of

12/16/22

Razvan Marinescu, Leung, Jeremy2

12/6/22

Start WESTPA from multiple initial states

Hi Razvan, Yes, it is possible. Please take a look at Section 3.1.3 in the following paper, which

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Start WESTPA from multiple initial states

Hi Razvan, Yes, it is possible. Please take a look at Section 3.1.3 in the following paper, which

12/6/22

Razvan Marinescu, … Jeremy Leung8

12/1/22

WESTPA + MPI - error on large 0.5 million atom system

Gotcha. Thanks Jeremy! On Wed, 30 Nov 2022 at 17:12, Jeremy Leung <jeremyl...@gmail.com>

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WESTPA + MPI - error on large 0.5 million atom system

Gotcha. Thanks Jeremy! On Wed, 30 Nov 2022 at 17:12, Jeremy Leung <jeremyl...@gmail.com>

12/1/22

Praveen Ranganath Prabhakar, Anthony Bogetti2

12/1/22

<WESTPA 2.0: Error while reading trajectories>

Hi Praveen, You seem to be on the right track with your code snippet. Can you try using the full path

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<WESTPA 2.0: Error while reading trajectories>

Hi Praveen, You seem to be on the right track with your code snippet. Can you try using the full path

12/1/22

Akshay, Jeremy Leung3

11/17/22

Help with assign.h5 (from w_assign/w_ipa)

Hello Jeremy, Thanks for addressing my queries and for all the tips. The 'coloring' scheme is

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Help with assign.h5 (from w_assign/w_ipa)

Hello Jeremy, Thanks for addressing my queries and for all the tips. The 'coloring' scheme is

11/17/22

Praveen Ranganath Prabhakar, … Daniel Zuckerman5

10/28/22

<WESTPA 2.0: Trajectories help>

Hi Prof. Daniel Zuckerman, Many thanks for the wonderful explanation. I am able to understand that

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<WESTPA 2.0: Trajectories help>

Hi Prof. Daniel Zuckerman, Many thanks for the wonderful explanation. I am able to understand that

10/28/22

reyhan akkaya, … Jeremy Leung3

9/27/22

init.sh is not working

Hi Akkaya, We have updated the NAMD tutorial to work with WESTPA 2.0 (v2022.XX). Do note that this

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init.sh is not working

Hi Akkaya, We have updated the NAMD tutorial to work with WESTPA 2.0 (v2022.XX). Do note that this

9/27/22

Yunhui Ge, Anthony Bogetti8

8/22/22

questions for WE setup

Hello Yunhui, For multi-node setups, please see our tutorial which uses the ZMQ work manager, which

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questions for WE setup

Hello Yunhui, For multi-node setups, please see our tutorial which uses the ZMQ work manager, which

8/22/22

Nell Karpinski, Leung, Jeremy2

8/11/22

Setting up WESTPA

Hi Neil, It seems likely that something is not formatted correctly in your west.cfg, under the `

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Setting up WESTPA

Hi Neil, It seems likely that something is not formatted correctly in your west.cfg, under the `

8/11/22

Praveen Ranganath Prabhakar, Leung, Jeremy2

8/10/22

<WESTPA 2.0: Tutorial help>

Hi Praveen, Thank you for testing out WESTPA and the tutorials. For tutorial 3.3, you do not need to

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<WESTPA 2.0: Tutorial help>

Hi Praveen, Thank you for testing out WESTPA and the tutorials. For tutorial 3.3, you do not need to

8/10/22

Akshay, … rus...@ohsu.edu8

8/6/22

msm_we: Stratified clustering gives "ModuleNotFoundError: No module named 'msm_we'" error

Thank you very much John, that solved my issue. On Friday, 5 August, 2022 at 9:41:35 pm UTC+5:30 rus.

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msm_we: Stratified clustering gives "ModuleNotFoundError: No module named 'msm_we'" error

Thank you very much John, that solved my issue. On Friday, 5 August, 2022 at 9:41:35 pm UTC+5:30 rus.

8/6/22

7/26/22

Stable release of WESTPA 2.0

Dear WESTPA users, I am pleased to announce the stable release of WESTPA 2.0! Key features of WESTPA

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Stable release of WESTPA 2.0

Dear WESTPA users, I am pleased to announce the stable release of WESTPA 2.0! Key features of WESTPA

7/26/22

Razvan Marinescu, MADASU PAVAN KUMAR4

7/13/22

Segmentation fault during WESTPA run

Thanks Pavan. I can look into it, but I really doubt that it's a permissions issue. Because it

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Segmentation fault during WESTPA run

Thanks Pavan. I can look into it, but I really doubt that it's a permissions issue. Because it

7/13/22

Razvan Marinescu, … Razvan Marinescu5

7/12/22

Warnings during a WESTPA 2.0 run

Hi Anthony, Actually, I managed to fix the above warnings (the way you suggested), by just copying

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Warnings during a WESTPA 2.0 run

Hi Anthony, Actually, I managed to fix the above warnings (the way you suggested), by just copying

7/12/22

Ashlin James Poruthoor2

7/7/22

multi_west tool error

Thanks a lot, @Jeremy for the solution: Did you use a custom system.py or adaptive.py? You'll

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multi_west tool error

Thanks a lot, @Jeremy for the solution: Did you use a custom system.py or adaptive.py? You'll

7/7/22

Razvan Marinescu, … Barmak Mostofian7

7/5/22

Max number of walkers & keep only fringe walkers

Hi Matt and Barmak, Thank you so much for the insightful answers. That all makes sense. So I'll

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Max number of walkers & keep only fringe walkers

Hi Matt and Barmak, Thank you so much for the insightful answers. That all makes sense. So I'll

7/5/22

Akshay, rus...@ohsu.edu3

5/6/22

msm_we: collectCoordinates.py -- bound.shape error

Hello John, Thanks a lot for addressing my query. A few lines were missing lines in the updated

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msm_we: collectCoordinates.py -- bound.shape error

Hello John, Thanks a lot for addressing my query. A few lines were missing lines in the updated

5/6/22

Daniel Zuckerman

4/19/22

WESTPA data club

The next data club will be April 18 (tomorrow), and so far this slot is available. The WESTPA data

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WESTPA data club

The next data club will be April 18 (tomorrow), and so far this slot is available. The WESTPA data

4/19/22

Andres Arango, Leung, Jeremy3

3/29/22

MAB error with westpa 2.0

Hi Jeremy, Thank you for your help, the integrated MAB scheme worked perfectly! Best, Andres On

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MAB error with westpa 2.0

Hi Jeremy, Thank you for your help, the integrated MAB scheme worked perfectly! Best, Andres On

3/29/22

Seungho Choe, Anthony Bogetti3

3/21/22

Hi Anthony, Thank you for your response. Let me try to attach west.h5(zip file) again. Best, Seungho

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Hi Anthony, Thank you for your response. Let me try to attach west.h5(zip file) again. Best, Seungho

3/21/22

Lexin Chen, Leung, Jeremy4

1/14/22

Hi Lexin, Glad you were able to fix it and everything worked out. We significantly restructured the

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Hi Lexin, Glad you were able to fix it and everything worked out. We significantly restructured the

1/14/22

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