High Interaction Energy Standard Deviation

[Raj Choudhary]

Dear Sir

While running the calculation to find out the Interaction Entropy, in many of the cases I am getting the following message:

WARNING: THE INTERACTION ENERGY STANDARD DEVIATION [ σ(Int. Energy) ]
IS GREATER THAN 3.6 kcal/mol (~15 kJ/mol). THUS, THE INTERACTION ENTROPY VALUES ARE
NOT RELIABLE. CHECK THIS PAPER FOR MORE INFO (https://doi.org/10.1021/acs.jctc.1c00374)

I am attaching a results.dat file for your reference.

Is there any specific way to deal with such systems having higher standard deviation values? 

[marioe911116]

This will depend on several factors... Usually, the researchers applying this method use restraints and that way the Internal Energy SD is lower... However this is tricky since it has been observed that different restraints produce different/lower entropy values... Another solution could be choosing a range where the internal energy is more stable...

hope this helps!

[Raj Choudhary]

Thanks...Can you elaborate how to apply the restraints? And, is it a reasonably acceptable practice to compare the interactions (protein/protein or protein/ligand) with the effective free energy values (delta H) and not brining the entropy corrections? 

[marioe911116]

This should help with the restraints (https://www.researchgate.net/post/Gromacs-2020-How-to-apply-restrain-and-constraint-on-heavy-atoms-or-backbone)

and yes, it is a reasonably acceptable practice to compare the interactions (protein/protein or protein/ligand) with the effective free energy values (delta H)

[Raj Choudhary]

Thank you so much for the help.

Warm regards.

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