GROMACS version:2023
GROMACS modification: No
Dear all
Why does the number of hydrogen bonds increase with temperature in my MD simulation, and why does the RDF peak height (related to hydrogen bonding) also increase instead of decreasing, while the diffusion coefficient correctly increases with temperature?
It’s not necessarily the case that hydrogen bonds have to decrease with temperature, maybe the higher temperature resulted in a change of conformation which allowed additional binding to occur (keep in mind that hydrophobic effects increase with temperature), to get a more definitive answer you could try identifying significantly different changes in conformation (maybe using tools like PCA) and identifying exactly which additional hydrogen bonds may have formed.
By PCA, do you mean Principal Component Analysis of the conformations during the trajectory؟
Yes (sorry for late reply)
Could a short run time cause this? I repeated the simulation, and with increasing temperature, the diffusion coefficient sometimes decreases whereas it should normally increase. However, no abnormal events are observed in the visualization RMSD, or stability plots.