westpa-users

Hi Jeremy, SUPER COOL! It worked with wedap version 0.0.8. I followed your installation and the

Hi Jeremy, Thank you for letting me know. That option would be useful if/when it's added. Best,

Hi Jeremy, I did some testing to pinpoint exactly when the seg faults occur. Below is what I found. I

Awesome, that works. Thanks Jeremy! On Friday, September 22, 2023 at 5:34:49 PM UTC-7 jml...@pitt.edu

okay thank you for your advice. actually the problem was that after i activate the WESTPA environment

Hi Ibrahim, I agree that it seems likely to come down to the hdfview, we have actually come into a

Hi Ibrahim, Let me answer in order. 1. Yes. The whole problem with loading with westpa.analysis is

Ibrahim, WE simulation requires the use of stochastic dynamics. For MD simulations, this is typically

Fengyang, I will correspond with you offline about your issues. Best, Lillian On Thu, Aug 31, 2023 at

Hi Ibrahim, You will have to use w_states, but that would not affect the recycling events that

Hi Ibrahim, Great! It's a GROMACS issue. The -nt 2 seems to allow GROMACS to run on two threads.

Hi Yanxiao, 1. This is exactly the same as how bins/target states are defined for a WESTPA simulation

Hi Ibrahim, That's safe to ignore. On some systems, python didn't shut down cleanly, leading

Yes thank you for your help Sent from Yahoo Mail on Android On Sun, 27 Aug 2023 at 10:12 pm, Leung,

Hi Hayden, Yes, there is a bit of redundancy there. The block of code that links the files is not

Hi Fengyang, Thank you for replying, Hayden. That is correct. Fengyang, for more information please

Hi Jeremy, Thanks, that explains it! Looks like everything is working as intended. Almost all of my

Hello Smriti, The "still not clean after cleaning" suggests that the clusters/microbins

Hi Marion, Thank you for your response. After trying your suggestion, I found that if I use adaptive.

Hello Chunzhi, For multiple basis states, you will need to organize your bstates folder differently (

Thanks Jeremy, I was not aware that the 30 MAB bins did not include the bins for the 3 special

Hello Jeremy, That fixed it. Thank you! Best, Antryg On Tuesday, June 20, 2023 at 12:06:22 PM UTC-4

Hi Darian! Thanks a lot! I just wanted to double-check! Thank you! Ashlin On Tuesday, 20 June 2023 at

Hi Jeremy, I'm afraid I did not answer your email. Sorry about that. Thanks for the clarification

Hi Chloe, Thanks for providing the test file. `west_current_iteration` is an attribute and I was able

Hey everyone, I may have solved the error, so for the moment never mind!!!! Thank you and sorry for

Hi Ibrahim, Yes, you can indeed set up grouping based on the pocket volume of the protein. For

Hi Jeremy, Thank you for your advice. It appears that the issue was largely related to the high

Hi Praveen, When you have 10 job submission files, you're technically stopping and restarting the

Hello WESTPA group, I'm hoping to clarify the merge/split process in WESTPA. I am in the process