What formula for Km is used for 8 replica simulations and the tutorial

[aminsagar]

Hello.
Very interesting work.
I am trying to follow the protocol and I have a small question.
The formula for calculating Km given in the paper is followed in the 16 replica simulations.

I am trying to understand how you derived the values of Km for the 8 replica simulations which are also given in the tutorial.

    bash gennewtop.sh 1.000 1.000 processed.top topol0.top
    bash gennewtop.sh 0.943 1.000 processed.top topol1.top
    bash gennewtop.sh 0.889 1.003 processed.top topol2.top
    bash gennewtop.sh 0.838 1.010 processed.top topol3.top
    bash gennewtop.sh 0.790 1.020 processed.top topol4.top
    bash gennewtop.sh 0.745 1.027 processed.top topol5.top
    bash gennewtop.sh 0.702 1.035 processed.top topol6.top
    bash gennewtop.sh 0.662 1.045 processed.top topol7.top

Thanks,
Amin.

[yumzhang17]

Hi Amin, Thank you for your interest in REST3. And your question is indeed valuable! I would like to address your question with the following three points: 1. The Km equation you showed is specifically designed and used for the 16-replica simulations. And the 8-replica scaling no longer follows that equation. 2. The 8-replica simulation is a ‘back-up’ validation process, which is based on all observations from the 16-replica simulations. 3. Based on point 2, we aim to retain the scaling used in 16-rep simulations as much as possible especially for the same temperature conditions in the 8-rep simulations. Additionally, temperature below 330 K remains unscaled, since they generate reasonable conformations for p53-TAD. Referred to the scaling values used in 16-replica, we re-assigned Km based on the neighboring conditions, like (the left is for 8-rep, right is 16-rep): K335 ~= (K330 + K342)/2 K355 = K355 K377 ~= K379 K400 ~= (K392+K406)/2 K424 ~= K420 K450 = K450 Please not that the Km (8-rep) values are not guaranteed to be the most optimal. However, our experiences suggest that the accuracy on the third decimal of Km had minimal impact. I hope this explanation can be helpful. Please don’t hesitate to contact me if there is any unclearness or you want some further clarifications :) Best, Yumeng

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On Jul 11, 2023, at 3:43 AM, aminsagar ***@***.***> wrote: Hello. Very interesting work. I am trying to follow the protocol and I have a small question. The formula for calculating Km given in the paper is followed in the 16 replica simulations. <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F33936658%2F252589781-d1fc6c59-d813-4a0c-9c01-c20007ff6501.png&data=05%7C01%7Cyumzhang%40umass.edu%7C5105e9c1ad704c1b424e08db81e27e27%7C7bd08b0b33954dc194bbd0b2e56a497f%7C0%7C0%7C638246582031176314%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=heaSBB5AuLL3fwgGZ%2FToYz2RQDiKmSJnu3VK1Nmyt44%3D&reserved=0> I am trying to understand how you derived the values of Km for the 8 replica simulations which are also given in the tutorial. bash gennewtop.sh 1.000 1.000 processed.top topol0.top bash gennewtop.sh 0.943 1.000 processed.top topol1.top bash gennewtop.sh 0.889 1.003 processed.top topol2.top bash gennewtop.sh 0.838 1.010 processed.top topol3.top bash gennewtop.sh 0.790 1.020 processed.top topol4.top bash gennewtop.sh 0.745 1.027 processed.top topol5.top bash gennewtop.sh 0.702 1.035 processed.top topol6.top bash gennewtop.sh 0.662 1.045 processed.top topol7.top Thanks, Amin. — Reply to this email directly, view it on GitHub <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fyumzhang17%2FREST3_tutorial%2Fissues%2F1&data=05%7C01%7Cyumzhang%40umass.edu%7C5105e9c1ad704c1b424e08db81e27e27%7C7bd08b0b33954dc194bbd0b2e56a497f%7C0%7C0%7C638246582031176314%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gu%2F%2F0xn4%2FgtlTSkXv5jO188dJu6CsH9Zmtq30bXOpdo%3D&reserved=0>, or unsubscribe <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAOZQM5ITR3OSYVRAF5Y5JWDXPT7ZLANCNFSM6AAAAAA2FSVBQ4&data=05%7C01%7Cyumzhang%40umass.edu%7C5105e9c1ad704c1b424e08db81e27e27%7C7bd08b0b33954dc194bbd0b2e56a497f%7C0%7C0%7C638246582031176314%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Vof3OseNHiTSXEOMiLAJ%2Fgl1gKsad9wjgFUIYlAQnrE%3D&reserved=0>. You are receiving this because you are subscribed to this thread.