Hello
I simulated water confined between graphene.
now, I do not know that how i calculate the number of hydrogen bonds per water molecule?
If you define “hydrogen bond” by some distance
criterion, you could use compute coord/atom with a suitable
cutoff and group definition to count them.
Steve
If you define "hydrogen bond" by some distance
criterion, you could use compute coord/atom with a suitable
cutoff and group definition to count them.
a pure distance criterion will likely not be acceptable.
VMD has a hydrogen bond analysis tool, if you name your atoms properly
and don't need periodicity.
otherwise, there should be a discussion in the mailing list archives
about using one of the dreiding hbond pair styles for collecting hbond
information using rerun.
axel