Interaction Entropy

[فاطمه بیانی‎]

Hello everyone, 

I am trying to calculate Interaction Entropy by gmx_MMPBSA but the results are not logical, is the number of frames important in calculating Interaction Entropy? Because when the number of frames in the mmgbsa.in file is considered to be 20, the results are almost logical, but if the whole frame is taken from the trajectory (250), the results are not good.

[Mario Ernesto]

Hi there! You have encountered one of the problem with the interaction entropy, and is the one related with the convergence of the entropy value... Probably the standard deviation of the interaction energy in your case is quite high and that's why you get different values depending on how many frames you chose.... See below some considerations worth to take into account when working with the interaction entropy method:

• The standard deviation of the interaction energy (σIE) should always be reported when using the Interaction Entropy method.
• The Interaction Entropy method should be avoided if σIE > ~ 3.6 kcal/mol because it is impossible to converge the exponential average.
• It is advisable to study how the Interaction Entropy depends on N by block averaging (which also provide an estimate of the precision of the calculated entropies).
• A sampling frequency of 10 fs, as reported in the original IE publication, seems to be 3–40 times too dense. A sampling frequency of 0.1 ps would be more appropriate.
• The Interaction Entropy results may vary depending on the system flexibility or whether constraints were used or not in the MD simulation. 

Check this publication (https://pubs.acs.org/doi/full/10.1021/acs.jctc.1c00374) for more details...

Cheers!

On Wed, Jan 26, 2022, 8:32 AM فاطمه بیانی <fatemeh...@gmail.com> wrote:

Hello everyone, 

I am trying to calculate Interaction Entropy by gmx_MMPBSA but the results are not logical, is the number of frames important in calculating Interaction Entropy? Because when the number of frames in the mmgbsa.in file is considered to be 20, the results are almost logical, but if the whole frame is taken from the trajectory (250), the results are not good.

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