About the reliable entropy calculation

[陳冠宇]

Dear Sir,

1. I would like to know how to reduce my data's sigma value of interaction entropy (IE).

2. Why the sigma value of IE (entropy) is different from the SD value of -TdeltaS (entropy)? one is higher than 3.6 kcal/mole (is it not reliable ?) and the other is 0.05. What is the difference between sigma and SD during IE estimation? Why do we need to consider the sigma of IE whether greater than 3.6 kcal/mol or not? Should we consider estimating the criteria of SD? 

3. The output data of energy after calculation showed "Average", "SD" and "SEM". Does the "Average" mean the "sum of energy during the period of frames/ number of frames" or the "sum of moving average of energy/ number of frames"?

4. Should we show the data with the mean (Average?) ± SD? or SEM? which one is right?

We are looking forward to hearing from you.

Thank you

Sincerely,

Mark

[Mario Sergio Valdes]

1. I would like to know how to reduce my data's sigma value of interaction entropy (IE).

Check this thread (https://groups.google.com/g/gmx_mmpbsa/c/LDz765e85K4/m/Rr_i0Q2MAQAJ)

 

2. Why the sigma value of IE (entropy) is different from the SD value of -TdeltaS (entropy)? one is higher than 3.6 kcal/mole (is it not reliable ?) and the other is 0.05. What is the difference between sigma and SD during IE estimation? Why do we need to consider the sigma of IE whether greater than 3.6 kcal/mol or not? Should we consider estimating the criteria of SD? 

Most of the information you request is explained and referenced in the documentation. Please review it carefully.
The σIE corresponds to the standard deviation of the interaction energy, while the SD corresponds to the standard deviation of the IE in the selected segment. You can review the article mentioned in the output warning. Basically, it is because from that value it is extremely difficult to have convergence.
The σIE is intended to show whether the calculation is reliable or not. The SD shows if the selected fragment is "convergent". 

 

3. The output data of energy after calculation showed "Average", "SD" and "SEM". Does the "Average" mean the "sum of energy during the period of frames/ number of frames" or the "sum of moving average of energy/ number of frames"?

Honestly, I do not know the second formula. In this case, Average = Mean

 

4. Should we show the data with the mean (Average?) ± SD? or SEM? which one is right?

This thread may help you (https://www.researchgate.net/post/Should_I_use_the_standard_deviation_or_the_standard_error_of_the_mean). It is common to use Average+SD, since SEM is affected by sample size, so it would not be appropriate to compare energy values getting from trajectories with different lengths. In any case, it would depend on how you will report the energy values and that you specify it in your report.

HTH!

Mario S.

 

[陳冠宇]

Dear Sir,

Thank you for the information

warm regards,

Mark

***********************************

Mark, Guan-Yu Chen (陳冠宇) 

中國醫藥大學附設醫院 1JG1醫研部中醫藥研究發展中心

中國醫藥研發中心

中國醫科大學附屬醫院

台灣

電話：+886- 4-22053366 分機。3316/5711

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Mario Sergio Valdes <mariosergi...@gmail.com> 於 2022年9月7日 週三 晚上10:39寫道：

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