Groups
Conversations
All groups and messages
Send feedback to Google
Help
Sign in
Groups
westpa-users
Conversations
Labels
About
westpa-users
1–30 of 309
Welcome to the WESTPA user's mailing list!
Mark all as read
Report abusive group
0 selected
Mac Kevin Braza
,
Jeremy Leung
5
Sep 27
wedap usage
Hi Jeremy, SUPER COOL! It worked with wedap version 0.0.8. I followed your installation and the
unread,
wedap usage
Hi Jeremy, SUPER COOL! It worked with wedap version 0.0.8. I followed your installation and the
Sep 27
Jonathan Borowsky
,
Jeremy Leung
3
Sep 27
MAB bin boundaries (WESTPA 2.0)
Hi Jeremy, Thank you for letting me know. That option would be useful if/when it's added. Best,
unread,
MAB bin boundaries (WESTPA 2.0)
Hi Jeremy, Thank you for letting me know. That option would be useful if/when it's added. Best,
Sep 27
Hayden Scheiber
, …
Jeremy Leung
16
Sep 27
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
unread,
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
Sep 27
Hayden Scheiber
,
Leung, Jeremy
5
Sep 25
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
unread,
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
Sep 25
Ibrahim Mohamed
,
Jeremy Leung
6
Sep 22
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
unread,
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
Sep 22
Ibrahim Mohamed
, …
Yang, Darian T
14
Sep 15
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
unread,
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
Sep 15
Ibrahim Mohamed
,
Leung, Jeremy
4
Sep 5
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
unread,
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
Sep 5
Ibrahim Mohamed
,
Lillian Chong
2
Sep 4
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
unread,
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
Sep 4
Han, Fengyang
,
Lillian Chong
2
Sep 1
Impact of Low Possibilty in simulation
Fengyang, I will correspond with you offline about your issues. Best, Lillian On Thu, Aug 31, 2023 at
unread,
Impact of Low Possibilty in simulation
Fengyang, I will correspond with you offline about your issues. Best, Lillian On Thu, Aug 31, 2023 at
Sep 1
Ibrahim Mohamed
,
Leung, Jeremy
2
Aug 29
can i change the value in tstate file between we iterations (just for tutorial purposes)
Hi Ibrahim, You will have to use w_states, but that would not affect the recycling events that
unread,
can i change the value in tstate file between we iterations (just for tutorial purposes)
Hi Ibrahim, You will have to use w_states, but that would not affect the recycling events that
Aug 29
Ibrahim Mohamed
,
Leung, Jeremy
6
Aug 29
How can i repeat a we iteration after removing it?
Hi Ibrahim, Great! It's a GROMACS issue. The -nt 2 seems to allow GROMACS to run on two threads.
unread,
How can i repeat a we iteration after removing it?
Hi Ibrahim, Great! It's a GROMACS issue. The -nt 2 seems to allow GROMACS to run on two threads.
Aug 29
Yanxiao Han
,
Leung, Jeremy
4
Aug 28
LPATH, Linguistics Pathway Analysis of Trajectories using Hierarchical clustering
Hi Yanxiao, 1. This is exactly the same as how bins/target states are defined for a WESTPA simulation
unread,
LPATH, Linguistics Pathway Analysis of Trajectories using Hierarchical clustering
Hi Yanxiao, 1. This is exactly the same as how bins/target states are defined for a WESTPA simulation
Aug 28
Ibrahim Mohamed
,
Leung, Jeremy
4
Aug 28
error while running the run.sh file for the nacl association in gromacs
Hi Ibrahim, That's safe to ignore. On some systems, python didn't shut down cleanly, leading
unread,
error while running the run.sh file for the nacl association in gromacs
Hi Ibrahim, That's safe to ignore. On some systems, python didn't shut down cleanly, leading
Aug 28
Ibrahim Mohamed
,
Leung, Jeremy
3
Aug 27
error in na cl association (while parsing a flow node did not find expected node content)
Yes thank you for your help Sent from Yahoo Mail on Android On Sun, 27 Aug 2023 at 10:12 pm, Leung,
unread,
error in na cl association (while parsing a flow node did not find expected node content)
Yes thank you for your help Sent from Yahoo Mail on Android On Sun, 27 Aug 2023 at 10:12 pm, Leung,
Aug 27
Anthony Bogetti
,
Hayden Scheiber
3
Aug 16
WESTPA-GROMACS tutorial now available
Hi Hayden, Yes, there is a bit of redundancy there. The block of code that links the files is not
unread,
WESTPA-GROMACS tutorial now available
Hi Hayden, Yes, there is a bit of redundancy there. The block of code that links the files is not
Aug 16
Han, Fengyang
, …
Anthony Bogetti
3
Aug 16
Specifying the smallest allowed weight not working
Hi Fengyang, Thank you for replying, Hayden. That is correct. Fengyang, for more information please
unread,
Specifying the smallest allowed weight not working
Hi Fengyang, Thank you for replying, Hayden. That is correct. Fengyang, for more information please
Aug 16
Praveen Ranganath Prabhakar
, …
Hayden Scheiber
15
Aug 9
MAB Recycing error
Hi Jeremy, Thanks, that explains it! Looks like everything is working as intended. Almost all of my
unread,
MAB Recycing error
Hi Jeremy, Thanks, that explains it! Looks like everything is working as intended. Almost all of my
Aug 9
Smriti P
,
Jeremy Leung
2
Jul 5
haMSM error while construction of flux matrix
Hello Smriti, The "still not clean after cleaning" suggests that the clusters/microbins
unread,
haMSM error while construction of flux matrix
Hello Smriti, The "still not clean after cleaning" suggests that the clusters/microbins
Jul 5
Fengyang Han
,
Han, Fengyang
6
Jun 30
Confused on "at" option in west.cfg in RecursiveBinMapper
Hi Marion, Thank you for your response. After trying your suggestion, I found that if I use adaptive.
unread,
Confused on "at" option in west.cfg in RecursiveBinMapper
Hi Marion, Thank you for your response. After trying your suggestion, I found that if I use adaptive.
Jun 30
Chunzhi Wu
,
Jeremy Leung
2
Jun 27
Unable to restart with multiple basis states
Hello Chunzhi, For multiple basis states, you will need to organize your bstates folder differently (
unread,
Unable to restart with multiple basis states
Hello Chunzhi, For multiple basis states, you will need to organize your bstates folder differently (
Jun 27
Ramon Crehuet
,
Jeremy Leung
3
Jun 21
Understanding number of bins with RecursiveBinMapper
Thanks Jeremy, I was not aware that the 30 MAB bins did not include the bins for the 3 special
unread,
Understanding number of bins with RecursiveBinMapper
Thanks Jeremy, I was not aware that the 30 MAB bins did not include the bins for the 3 special
Jun 21
Antryg Benedict
,
Jeremy Leung
3
Jun 20
Error basic nacl amber ZMQ tutorial
Hello Jeremy, That fixed it. Thank you! Best, Antryg On Tuesday, June 20, 2023 at 12:06:22 PM UTC-4
unread,
Error basic nacl amber ZMQ tutorial
Hello Jeremy, That fixed it. Thank you! Best, Antryg On Tuesday, June 20, 2023 at 12:06:22 PM UTC-4
Jun 20
Ashlin James Poruthoor
,
Yang, Darian T
4
Jun 20
w_ipa -ao error
Hi Darian! Thanks a lot! I just wanted to double-check! Thank you! Ashlin On Tuesday, 20 June 2023 at
unread,
w_ipa -ao error
Hi Darian! Thanks a lot! I just wanted to double-check! Thank you! Ashlin On Tuesday, 20 June 2023 at
Jun 20
Ramon Crehuet
, …
Jeremy Leung
5
Jun 20
Is a RecursiveBinMapper needed?
Hi Jeremy, I'm afraid I did not answer your email. Sorry about that. Thanks for the clarification
unread,
Is a RecursiveBinMapper needed?
Hi Jeremy, I'm afraid I did not answer your email. Sorry about that. Thanks for the clarification
Jun 20
Chloe Sheen
,
Jeremy Leung
2
May 17
truncating a partially corrupt h5 file
Hi Chloe, Thanks for providing the test file. `west_current_iteration` is an attribute and I was able
unread,
truncating a partially corrupt h5 file
Hi Chloe, Thanks for providing the test file. `west_current_iteration` is an attribute and I was able
May 17
Albert Ortega
2
May 16
The pcoords plotted don't match the ones I trace
Hey everyone, I may have solved the error, so for the moment never mind!!!! Thank you and sorry for
unread,
The pcoords plotted don't match the ones I trace
Hey everyone, I may have solved the error, so for the moment never mind!!!! Thank you and sorry for
May 16
Ibrahim Mohamed
,
Lillian Chong
2
May 15
can i use binless sampling to study conformations of a protein?
Hi Ibrahim, Yes, you can indeed set up grouping based on the pocket volume of the protein. For
unread,
can i use binless sampling to study conformations of a protein?
Hi Ibrahim, Yes, you can indeed set up grouping based on the pocket volume of the protein. For
May 15
Han, Fengyang
, …
Jeremy Leung
9
May 11
Issues Encountered While Using WESTPA with AMBER for the 7.2 Tutorial on Pitt CRC GPU
Hi Jeremy, Thank you for your advice. It appears that the issue was largely related to the high
unread,
Issues Encountered While Using WESTPA with AMBER for the 7.2 Tutorial on Pitt CRC GPU
Hi Jeremy, Thank you for your advice. It appears that the issue was largely related to the high
May 11
Praveen Ranganath Prabhakar
, …
Jeremy Leung
4
May 10
Reweighing code query
Hi Praveen, When you have 10 job submission files, you're technically stopping and restarting the
unread,
Reweighing code query
Hi Praveen, When you have 10 job submission files, you're technically stopping and restarting the
May 10
Chloe Sheen
May 9
merging walkers with different histories for MFPT calculation
Hello WESTPA group, I'm hoping to clarify the merge/split process in WESTPA. I am in the process
unread,
merging walkers with different histories for MFPT calculation
Hello WESTPA group, I'm hoping to clarify the merge/split process in WESTPA. I am in the process
May 9