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Fernando Amrein
, …
Leung, Jeremy
16
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 Chong
3
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 Bogetti
2
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, Jeremy
3
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 Bogetti
6
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 Marinescu
12
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 Marinescu
2
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, Jeremy
7
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, Jeremy
4
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, Jeremy
4
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, Jeremy
2
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 Leung
8
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 Bogetti
2
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 Leung
3
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 Zuckerman
5
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 Leung
3
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 Bogetti
8
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, Jeremy
2
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, Jeremy
2
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.edu
8
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
Lillian Chong
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 KUMAR
4
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 Marinescu
5
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 Poruthoor
2
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 Mostofian
7
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.edu
3
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, Jeremy
3
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 Bogetti
3
3/21/22
w_pdist error
Hi Anthony, Thank you for your response. Let me try to attach west.h5(zip file) again. Best, Seungho
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w_pdist error
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, Jeremy
4
1/14/22
w_succ error
Hi Lexin, Glad you were able to fix it and everything worked out. We significantly restructured the
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w_succ error
Hi Lexin, Glad you were able to fix it and everything worked out. We significantly restructured the
1/14/22