IE calculation for the clustered trajectory file

[Xu Pan]

Dear all,

I am new to using gmx_MMPBSA, so perhaps this is a naive question. So far, I have been trying to use gmx_MMPBSA to calculate the interaction entropy. However, I have obtained a very high -TΔS value, as shown in the attached picture.

Could this be because I did not use a continuous trajectory file? If so, how can I improve this?

Best regards,

Xu Pan

[marioe911116]

The sigma value, which is related to the stabaility of the interaction energy is quite high, and thta's the reason for such high interaction entropy. This is one of the limitation of this method. More info in this paper:

https://pubs.acs.org/doi/full/10.1021/acs.jctc.1c00374

[Xu Pan]

Dear sir,

Thank you very much.

2024年7月12日金曜日 2:24:47 UTC+9 marioe911116: