How to estimate H-Bond energy in gromacs

User discussions
1

I would like to quantify H-Bond energy and apolar solvation energy for my system (a protein chain). The latter can be estimated by g_mmpbsa. But it seems that the H-Bond energy cannot be estimated either by gmx or by g_mmpbsa…?
Is there a method to achieve this?

Many thanks!

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2

The quantities you are asking for are now well defined. Those appear in simplified models that decompose free-energies to be able to compute fre-energies in a faster, simplified way. In reality, interactions between atoms and molecules arise from electrostatic and Van der Waals interactions. Those can not be uniquely decomposed in e.g. H-bond and apolar solvation energies. The energy of and H-bond in e.g. water depends on the definition. If you have very precise definitions for the quantities you are interested in, you might be able to compute them.

3

Thanks very much :)
I use Gromacs’ built-in criterion to determine hydrogen bonds. How to compute the energy?

4

Hi, Liujy!
Have you found the way to estimate H-Bond energy? I am also curious about this problem.I tried to estimate the H-Bond energy to be the electrostatic energy between the Hydrogen and acceptor atom ,but the strength is too large( around 200 kJ/mol).

5

I did not find a way to estimate H-Bond energy… It seems that we cannot estimate purely H-Bond energy by Gromacs if there are other types of interaction between residues.

6

Thanks for you information! Good luck!